Phylogenetics of the brachyuran crabs (Crustacea: Decapoda): The status of Podotremata based on small subunit nuclear ribosomal RNA

Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group

Despite extensive morphological and molecular studies, the phylogenetic interrelationships within the infraorder Brachyura and the phylogenetic positions of many taxa remain uncertain. Studies that used a limited number of molecular markers have often failed to provide sufficient resolution, and may be susceptible to stochastic errors and incomplete lineage sorting (ILS). Here we reconstructed the phylogenetic relationships within the Brachyura using transcriptome data of 56 brachyuran species, including 14 newly sequenced taxa. Five supermatrices were constructed in order to exclude different sources of systematic error. The results of the phylogenetic analyses indicate that Heterotremata is non-monophyletic, and that the two Old World primary freshwater crabs (Potamidae and Gecarcinucidae) and the Hymenosomatoidea form a clade that is sister to the Thoracotremata, and outside the Heterotremata. We also found that ILS is the main cause of the gene-tree discordance of these freshwater crabs. Divergence time estimations indicate that the Brachyura has an ancient origin, probably either in the Triassic or Jurassic, and that the majority of extant families and superfamilies first appeared during the Cretaceous, with a constant increase of diversity in Post-Cretaceous-Palaeogene times. The results support the hypothesis that the two Old World freshwater crab families included in this study (Potamidae and Gecarcinucidae) diverged from their marine ancestors around 120 Ma, in the Cretaceous. In addition, this work provides new insights that may aid in the reclassification of some of the more problematic brachyuran groups.

Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least 7 and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways. [Brachyura; convergent evolution; crustaceans; divergence times; fossil calibration; molecular phylogeny; terrestrialization; threshold model.].

The analyses of the complete mitochondrial genomes of three crabs revealed novel gene rearrangements and phylogenetic relationships of Brachyura

BACKGROUND

Brachyura crab is the largest branch of Decapoda crustacean. Phylogenetic relationships within Brachyura remain controversial to be investigated. The mitochondrial genome (mitogenome) is an important molecular marker for studying the phylogenetic relationships of Brachyura.

METHODS AND RESULTS

To understand the phylogeny of Brachyura, the three complete mitogenomes from Charybdis annulata, Leptodius exaratus, and Spider crab were sequenced and annotated. Their full length was 15,747, 15,716, and 16,608 bp long, respectively. The first two crabs both contained 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. However, Spider crab contained 13 PCGs, two rRNA genes, 25 tRNA genes and a control region. The mitogenomes of each of the three crabs exhibited high AT content (67.8%, 69.1%, and 70.8%), with negative AT skews (-0.014, - 0.028, and - 0.017) and GC skews (-0.269, - 0.286, and - 0.341). The gene order of C. annulata was identical to the ancestor of Brachyura. Compared with the ancestor of Brachyura, L. exaratus exhibited the gene rearrangements of Val (V)-rrnS-control region, and Spider crab had the four copies of Lys (K). Phylogenetic analyses indicated that C. annulata belonged to Portunidae family, Portunoidea superfamilies, L. exaratus belonged to Xanthidae family, Xanthoidea superfamilies, and Spider crab belonged to Mithracidae family, Majoidea superfamilies. Phylogenetic analyses showed that the two species (Somanniathelphusa boyangensis and Huananpotamon lichuanense) belonging to the Potamoidea were sister groups to the Thoracotremata, thus supporting the conclusion that Heterotremata is polyphyletic.

CONCLUSION

The results of this study enriched the crab mitogenome database and enabled us to better understand the phylogenetic relationships of Brachyura.

The Complete Mitochondrial Genome of Pilumnopeus Makianus (Brachyura: Pilumnidae), Novel Gene Rearrangements, and Phylogenetic Relationships of Brachyura

Pilumnopeus makianus is a crab that belongs to Pilumnidae, Brachyura. Although many recent studies have focused on the phylogeny of Brachyura, the internal relationships in this clade are far from settled. In this study, the complete mitogenome of P. makianus was sequenced and annotated for the first time. The length of the mitogenome is 15,863 bp, and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and 2 ribosomal RNA genes (rRNA). The mitogenome exhibits a high AT content (72.26%), with a negative AT-skew (-0.01) and a GC-skew (-0.256). In the mitogenome of P. makianus, all the tRNA genes are folded into the typical cloverleaf secondary structure, except trnS1 (TCT). A comparison with the ancestors of Brachyura reveals that gene rearrangement occurred in P. makianus. In addition, phylogenetic analyses based on thirteen PCGs indicated that P. makianus, Pilumnus vespertilio, and Echinoecus nipponicus clustered into a well-supported clade that supports the monophyly of the family Pilumnidae. These findings enabled a better understanding of phylogenetic relationships within Brachyura.

Ecological Transitions and the Shape of the Decapod Tree of Life

Understanding the processes that shaped the distribution of species richness across the Tree of Life is a central macroevolutionary research agenda. Major ecological innovations, including transitions between habitats, may help to explain the striking asymmetries of diversity that are often observed between sister clades. Here, we test the impact of such transitions on speciation rates across decapod crustaceans, modelling diversification dynamics within a phylogenetic framework. Our results show that, while terrestrial lineages have higher speciation rates than either marine or freshwater lineages, there is no difference between mean speciation rates in marine and freshwater lineages across Decapoda. Partitioning our data by infraorder reveals that those clades with habitat heterogeneity have higher speciation rates in freshwater and terrestrial lineages, with freshwater rates up to 1.5 times faster than marine rates, and terrestrial rates approximately four times faster. This averaging out of marine and freshwater speciation rates results from the varying contributions of different clades to average speciation rates. However, with the exception of Caridea, we find no evidence for any causal relationship between habitat and speciation rate. Our results demonstrate that while statistical generalisations about ecological traits and evolutionary rates are valuable, there are many exceptions. Hence, while freshwater and terrestrial lineages typically speciate faster than their marine relatives, there are many atypically slow freshwater lineages and fast marine lineages across Decapoda. Future work on diversification patterns will benefit from the inclusion of fossil data, as well as additional ecological factors.

The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura

Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.

Redescription of the hermit crab Diogenes pugilator (Decapoda: Anomura) reveals the existence of a species complex in the Atlanto-Mediterranean transition zone, resulting in the resurrection of D. curvimanus and the description of a new species

Examination of material from the coasts of the Iberian Peninsula and nearby areas has revealed that more than one species is mixed under the name for the common diogenid hermit crab, Diogenes pugilator. In this study, three species are recognized, primarily on the basis of a combination of morphological characters and live colour patterns. Diogenes pugilator is redescribed on the basis of a neotype selected from near the supposed type locality, as well as specimens from other localities. Diogenes curvimanus is resurrected and the name attributed to a second species, whereas a third morphotype is described as a new species, Diogenes armatus sp. nov.. The last two species are also fully described and differentiating characters among the three species are discussed. Newly generated sequences from two mitochondrial genes and one nuclear gene, and comparative analyses with other available DNA sequences for the genus, are also included. The corresponding molecular phylogenies support the recognition of the three species and suggest the presence of additional unknown species in the D. pugilator species complex. All previous records of D. pugilator should be revised in the light of these new findings. Finally, a comprehensive identification key to the eastern Atlantic and western Mediterranean species of Diogenes is also provided.

Crab in amber reveals an early colonization of nonmarine environments during the Cretaceous

Amber fossils provide snapshots of the anatomy, biology, and ecology of extinct organisms that are otherwise inaccessible. The best-known fossils in amber are terrestrial arthropods—principally insects—whereas aquatic organisms are rarely represented. Here, we present the first record of true crabs (Brachyura) in amber—from the Cretaceous of Myanmar [~100 to 99 million years (Ma)]. The new fossil preserves large compound eyes, delicate mouthparts, and even gills. This modern-looking crab is nested within crown Eubrachyura, or “higher” true crabs, which includes the majority of brachyuran species living today. The fossil appears to have been trapped in a brackish or freshwater setting near a coastal to fluvio-estuarine environment, bridging the gap between the predicted molecular divergence of nonmarine crabs (~130 Ma) and their younger fossil record (latest Cretaceous and Paleogene, ~75 to 50 Ma) while providing a reliable calibration point for molecular divergence time estimates for higher crown eubrachyurans.

How to become a crab: Phenotypic constraints on a recurring body plan

A fundamental question in biology is whether phenotypes can be predicted by ecological or genomic rules. At least five cases of convergent evolution of the crab-like body plan (with a wide and flattened shape, and a bent abdomen) are known in decapod crustaceans, and have, for over 140 years, been known as "carcinization." The repeated loss of this body plan has been identified as "decarcinization." In reviewing the field, we offer phylogenetic strategies to include poorly known groups, and direct evidence from fossils, that will resolve the history of crab evolution and the degree of phenotypic variation within crabs. Proposed ecological advantages of the crab body are summarized into a hypothesis of phenotypic integration suggesting correlated evolution of the carapace shape and abdomen. Our premise provides fertile ground for future studies of the genomic and developmental basis, and the predictability, of the crab-like body form.

Characterization of the complete mitochondrial genome of convex reef crab Carpilius convexus (Forskål, 1775)

The complete mitochondrial genome of convex reef crab Carpilius convexus was determined and characterized for the first time from the South China Sea. The whole mitogenome is 15,766 bp long and consists of 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes (PCGs), and 1 control region. The nucleotide composition of the mitogenome is significantly biased (A, G, T, and C is 36.91%, 17.94%, 34.95%, and 10.19%, respectively) with A + T contents of 71.86%. All PCGs start with a normal initiation codon ATN and terminate with a standard stop codon except ND1 gene end with TTG. Five microsatellites are identified in C. convexus mitogenome sequences. The phylogenetic tree showed that C. convexus was first clustered with Carpilius maculatus, and strongly supports that the recognition of the Carpiliidae as a monophyletic family.

The complete mitochondrial genome of Calappa bilineata: The first representative from the family Calappidae and its phylogenetic position within Brachyura

In this study, we determined the complete mitogenome sequence of Calappa bilineata, which is the first mitogenome of Calappidae up to now. The total length is 15,606 bp and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and one control region. The genome composition is highly A + T biased (68.7%), and exhibits a negative AT-skew (-0.010) and GC-skew (-0.267). As with other invertebrate mitogenomes, the PCGs start with the standard ATN and stop with the standard TAN codons or incomplete T. Phylogenetic analysis showed that C. bilineata was most closely related to Matuta planipes (Matutidae), and these two species formed a sister clade, constituting a Calappoidea group and forming a sister clade with part of Eriphioidea. The existence of the polyphyletic families raised doubts over the traditional classification system. These results will help to better understand the features of the C. bilineata mitogenome and lay foundation for further evolutionary relationships within Brachyura.

DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity

Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crustaceans are often associated with varied habits, forms, sizes and habitats; making species identification by conventional methods extremely challenging. In addition, progress towards understanding the diversity within this group especially in southern Africa has been severely hampered by the declining number of trained taxonomists, the presence of invasive alien species, over exploitation, etc. However, the advent of molecular techniques such as “DNA barcoding and Metabarcoding” can accelerate species identification and the discovery of new species. To contribute to the growing body of knowledge on crustacean diversity, we collected data from five southern African countries and used a DNA barcoding approach to build the first DNA barcode reference library for southern African crustaceans. We tested the reliability of this DNA barcode reference library to facilitate species identification using two approaches. We recovered high efficacy of specimen identification/discrimination; supported by both barcode gap and tree-base species identification methods. In addition, we identified alien invasive species and specimens with ‘no ID” in our DNA barcode reference library. The later; highlighting specimens requiring (i) further investigation and/or (ii) the potential presence of cryptic diversity or (iii) misidentifications. This unique data set although with some sampling gaps presents many opportunities for exploring the effect and extent of invasive alien species, the role of the pet trade as a pathway for crustacean species introduction into novel environments, sea food authentication, phylogenetic relationships within the larger crustacean groupings and the discovery of new species.

Exceptional preservation of mid-Cretaceous marine arthropods and the evolution of novel forms via heterochrony

Evolutionary origins of novel forms are often obscure because early and transitional fossils tend to be rare, poorly preserved, or lack proper phylogenetic contexts. We describe a new, exceptionally preserved enigmatic crab from the mid-Cretaceous of Colombia and the United States, whose completeness illuminates the early disparity of the group and the origins of novel forms. Its large and unprotected compound eyes, small fusiform body, and leg-like mouthparts suggest larval trait retention into adulthood via heterochronic development (pedomorphosis), while its large oar-like legs represent the earliest known adaptations in crabs for active swimming. Our phylogenetic analyses, including representatives of all major lineages of fossil and extant crabs, challenge conventional views of their evolution by revealing multiple convergent losses of a typical "crab-like" body plan since the Early Cretaceous. These parallel morphological transformations may be associated with repeated invasions of novel environments, including the pelagic/necto-benthic zone in this pedomorphic chimera crab.

Comparative spermatozoal ultrastructure and molecular analysis in dromiid crabs and their phylogenetic implications for Dromiidae and Podotremata (Decapoda: Brachyura)

We described the spermatozoal ultrastructure and conducted a molecular analysis of Dromiidae Hypoconcha parasitica, Hypoconcha arcuata, Moreiradromia antillensis and Dromia erythropus. To elucidate the relationship between the different species of this brachyuran group, we also compared the spermatozoal morphologies and phylogenetic positioning among species of Dromiidae, Dromioidea and Podotremata. Specimens were collected from the northern coast of São Paulo, Brazil and were fixed and processed followed by transmission electron microscopy and molecular analysis routines. The Dromiidae spermatozoa studied are characterized by a discoidal acrosome, with three or four concentric zones, which are centrally separated by a bilaterally capitate perforatorial chamber, with a "mushroom"-shaped apex in the Hypoconchinae and a "T-shape" in Dromiinae. Above the perforatorial chamber, there is an apical protuberance, continuous with the subopercular region and the operculum, which forms a low, centrally perforated dome. Under differential interference contrast microscopy, the spermatozoa show 3 to 4 radial arms. The spermatozoal characters in Hypoconchinae and Dromiinae do not separate these subfamilies from the Dromiidae and Dromioidea. Ultrastructural differentiation was only found between representative Dromioidea and other Podotremata. Thus, the spermiotaxonomy of these Hypoconcha, Moreiradromia and Dromia species corroborated previous morphological and molecular studies, supporting the monophyly of Dromiidae and Dynomenidae in relation to Homolidae and Latreilliidae.

Seminal fluid production and sperm packaging in dromiid crabs (Brachyura, Podotremata)

Reproductive anatomy, including sperm storage structures and sperm transfer, is an important feature used to analyze phylogenetic relationships among taxa. We describe the male reproductive anatomy, seminal fluid production and packaging of spermatozoa in the vas deferens of primitive crabs. In all species of Dromiidae, the testes were tubular type and the vas deferens is a tube with a simple epithelium. The spermatozoa are in a central mass immersed in type I secretion, forming a large spermatic cord. In Moreiradromia antillensis and Dromia erythropus the spermatic cord is surrounded by a more complex secretion layer composed by protein granules and polysaccharides that seem to be responsible to form the sperm plaque which was absent in Hypoconcha. The sperm plaque was found in all Dromiinae species, which may result from the mating and probably act as a barrier to subsequent copulations. These patterns of elongated coenospermic spermatophore found here are unique and different from the spermatophores of all true crabs and may be considered a plesiomorphic state to spermatophoric structure in Brachyura. Our results show a novel type of spermatozoa packaging and new insights into how sperm might be transferred in Podotremata.

Comparative transcriptome analysis of Eriocheir japonica sinensis response to environmental salinity

Chinese mitten crabs (Eriocheir japonica sinensis) are catadromous, spending most of their lives in fresh water, but moving to a mixed salt-fresh water environment for reproduction. The characteristics of this life history might imply a rapidly evolutionary transition model for adaptation to marine from freshwater habitats. In this study, transcriptome-wide identification and differential expression on Chinese mitten crab groups were analysed. Results showed: clean reads that were obtained totalled 93,833,096 (47,440,998 in Group EF, the reference, and 46,392,098 in Group ES, the experimental) and 14.08G (7.12G in Group EF 6.96G in Group ES); there were 11,667 unigenes (15.29%) annotated, and they were located to 230 known KEGG pathways in five major categories; in differential expression analysis, most of the top 20 up-regulated pathways were connected to the immune system, disease, and signal transduction, while most of the top 20 down-regulated pathways were related to the metabolism system; meanwhile, 8 representative osmoregulation-related genes (14-3-3 epsilon, Cu2+ transport ATPase, Na+/K+ ATPase, Ca2+ transporting ATPase, V-ATPase subunit A, Putative arsenite-translocating ATPase, and Cation transport ATPase, Na+/K+ symporter) showed up-regulation, and 1 osmoregulation-related gene (V-ATPase subunit H) showed down-regulation. V-ATPase subunit H was very sensitive to the transition of habitats. These results were consistent with the tests of qRT-PCR. The present study has provided a foundation to further understand the molecular mechanism in response to salinity changing in water.

Adaptively differential expression analysis in gill of Chinese mitten crabs (Eriocheir japonica sinensis) associated with salinity changes

Desalination of marine species has become an important development direction for aquaculture in China and other countries. However, that how to regulate the salt balance to adapt to new freshwater habitats is a serious challenge for marine species in desalination of aquaculture. In the study, Chinese mitten crabs (Eriocheir japonica sinensis) was selected to analyse the adaptively differential expression in salinity changes for their novel characteristics of life history. The results showed that gill was the most relevant tissue in osmoregulation that was validated by biomarkers (Na⁺/K⁺-ATP, V-type H⁺-ATPase) with qPCR. Na⁺/K⁺-ATPase is a primary transporter and maintains the body fluid osmolality by actively pumping Na⁺ to the hemolymph, and V-type H⁺-ATPase is responsible for acid-base balance and nitrogen excretion. So both transcriptome data and qPCR results showed the significantly differential expression of Na⁺/K⁺-ATPase and V-type H⁺-ATPase in gills. Moreover, NAK-α had the most significantly differential expression level in salinity change, and other genes such as GST, HSP90, S27, UBE, VATB also revealed significantly up-regulation. They are considered the key enzymes during the transition from a marine environment to land. Present results have provided a foundation to further understand the molecular adaptive mechanism in desalination of marine species.

The reproductive system of Limnopilos naiyanetri indicates a thoracotreme affiliation of Hymenosomatidae (Decapoda, Eubrachyura)

The eubrachyuran Hymenosomatoidea is widely distributed in tropical and subtropical regions ranging from marine to freshwater habitats. Even though the biology of this taxon has been studied to some extent, its phylogenetic relationships are not resolved. Based on different morphological characters, some authors suggested a close affinity of hymenosomatid crabs to heterotremes. However, many of these characters are ambiguous, and the few molecular studies did not provide convincing solutions either. To address this issue, we studied the reproductive system of the hymenosomatid freshwater species Limnopilos naiyanetri Chuang and Ng, 1991 using histology and scanning electron microscopy. The females show the characteristic organization of the paired eubrachyuran reproductive system. Additionally, a bursa (an accessory sperm storing cuticle cavity) is present. The male copulatory system is characterized by paired long first and short second gonopods, and a pair of sternal gonopores equipped with a penis. Both, the female and male reproductive organs reveal a number of similarities to thoracotreme crabs. The seminal receptacle is lined by a very thin cuticle and by a mono-layered glandular epithelium. The male gonopods and the sternal genital opening also resemble the thoracotreme condition. Thus, our results indicate that Hymenosomatidae are most likely part of the Thoracotremata.

Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution

Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.

Paradorippe granulata - A crab with external fertilization and a novel type of sperm storage organ challenges prevalent ideas on the evolution of reproduction in Eubrachyura (Crustacea: Brachyura: Dorippidae)

Two fundamentally different sperm storage organs occur in Brachyura. The probably paraphyletic podotremes show intersegmental spermathecae, which are distant from oviducts and coxal gonopores. Hence, fertilization is external. In contrast to this, the seminal receptacles of Eubrachyura are directly connected with the ovaries. Thus, at least initial fertilization is internal. This pattern has been interpreted as an apomorphy of Eubrachyura. To test this hypothesis, we studied the morphology of the reproductive organs of Paradorippe granulata, a representative of the putatively early diverging eubrachyuran lineage Dorippoidea. Applying histology, 3D-reconstructions and micro-computed-tomography we revealed a novel type of sperm storage organ. Female P.granulata lack the characteristic eubrachyuran seminal receptacle. Instead sperm is stored in four cuticle-lined bursae, two on each side of the paired oviducts. The elaborate bulbous male gonopod with several terminal processes is adapted to transferring sperm into the female twin bursae. Since oviducts and twin bursae are not directly connected, spermatozoa and oocytes mix when gametes pass through the sternal vulva. Thus, fertilization in P.granulata is external. Our finding of a eubrachyuran crab that lacks seminal receptacles and exhibits external fertilization calls prevailing concepts on the evolution of sperm storage in Eubrachyura into question.

Characterisation of the complete mitochondrial genome of Helice wuana (Grapsoidea: Varunidae) and comparison with other Brachyuran crabs

The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0.036) and GC-skew (-0.269) among Brachyura crabs. Gene rearrangements were detected, as was tandem duplication followed by random loss, which explains the translocation of mitochondrial genes. Phylogenetic analysis showed that H. wuana and H. tientsinensis clustered on one branch with high nodal support values. These results confirm that the placement of H. wuana within the Varunidae family of Thoracotrematan crabs. This study will provided a better understanding for gene rearrangements and crab evolution in the further.

Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae)

Recent morphological and molecular evidence has challenged classical interpretations of eubrachyuran phylogeny and evolution. Complete mitochondrial genomes of two species of potamid freshwater crabs, Sinopotamon yaanense and Sinopotamon yangtsekiense were obtained using next-generation sequencing. The results revealed a novel gene order with translocations of a five-gene block and a tRNA gene in comparison to available brachyuran mitochondrial genomes. DNA sequence comparisons position the Potamidae, a primary freshwater crab family, outside of the clade for the traditional heterotreme families, and closer to the clade that includes the thoracotreme families of grapsoid and ocypodoid crabs. Mitogenomic comparisons using rapid next-generation sequencing and a much wider taxonomic sample are required for a high-resolution examination of the phylogenetic relationships within the Eubrachyura.

Phylogenetic implications of sperm storage in Podotremata: Histology and 3D-reconstructions of spermathecae and gonopores in female carrier crabs (Decapoda: Brachyura: Homoloidea)

Female reproductive systems are important characters for understanding the evolution of Brachyura and resolving its phylogenetic relationships. We herein investigate a podotreme brachyuran reproductive system comprehensively for the first time studying spermathecae and gonopores of Homoloidea with histological methods, micro-computer tomography and scanning electron microscopy. Our results show that spermathecal apertures are species-specific and their shape corresponds closely to that of male copulatory organs. Apertures were either enclosed by membranous cuticle areas or otherwise occluded preventing direct access into spermathecae. 3D-reconstructions reveal that spermathecae differ between the species Paromola cuvieri and Homola barbata with regard to the involvement of sternite 7 and 8, respectively, in forming the sperm storage chamber. The cuticle epithelium that lines the spermathecal chamber is irregular and distinct from the remaining cylindrical cuticle epithelium. A first uniramous pleopod was present in all homoloids studied and always held in a position to cover spermathecal apertures. Specific pulvinated cuticle structures present on both sides of the first pleopod are herein interpreted as adhesive structures functioning in reproductive processes. The coxal gonopores were enclosed by a laterally arising muscular mobile operculum that resembles opercula described in eubrachyuran vaginae, which raises the question whether these two structures are homologous. Our results are compared with data available for other brachyuran groups and discussed in terms of phylogenetic relationships within the Brachyura and possible functions in insemination and fertilization in Podotremata. J. Morphol. 278:89-105, 2017. ©© 2016 Wiley Periodicals,Inc.

A new type of brachyuran seminal receptacle in the masked crab Ethusa mascarone (Brachyura, Ethusidae)

The reproductive system of the female Ethusa mascarone was studied with a combination of histological and MRI-techniques. The study reveals a completely new type of eubrachyuran seminal receptacle. This receptacle consists of two largely separate chambers that engage with each other in a manner similar to shaking hands. One chamber facing the medial axis is lined by cuticle while the second chamber consists of a thick holocrine epithelium. Both chambers are connected by two openings of a unique structure. First, the glandular chamber opens ventro-laterally to the cuticle chamber via a laterally flattened connective duct that is lined by a highly folded cuticle. A second opening connects both chambers dorsally with the oviduct orifice. A distinct character is the cuticular hook-like projection that is situated in between the connection of oviduct opening, the glandular chamber and the cuticle chamber of the seminal receptacle. The complete seminal receptacle exhibits a combination of plesiomorphic and apomorphic characters. The arrangement of the receptacles featured in two separate chambers, including the ventro-lateral connection of the glandular chamber to the cuticle chamber, presumably reflects an early evolutionary stage of an eubrachyuran receptacle. In contrast, the dorso-lateral opening between both chambers, including the hook-like projection, appears to be an apomorphic character of at least E. mascarone. J. Morphol. 277:1497-1508, 2016. © 2016 Wiley Periodicals, Inc.

A 150-million-year-old crab larva and its implications for the early rise of brachyuran crabs

True crabs (Brachyura) are the most successful group of decapod crustaceans. This success is most likely coupled to their life history, including two specialised larval forms, zoea and megalopa. The group is comparably young, starting to diversify only about 100 million years ago (mya), with a dramatic increase in species richness beginning approximately 50 mya. Early evolution of crabs is still very incompletely known. Here, we report a fossil crab larva, 150 mya, documented with up-to-date imaging techniques. It is only the second find of any fossil crab larva, but the first complete one, the first megalopa, and the oldest one (other fossil ca. 110 mya). Despite its age, the new fossil possesses a very modern morphology, being indistinguishable from many extant crab larvae. Hence, modern morphologies must have been present significantly earlier than formerly anticipated. We briefly discuss the impact of this find on our understanding of early crab evolution.

The complete mitochondrial genomes of Umalia orientalis and Lyreidus brevifrons: The phylogenetic position of the family Raninidae within Brachyuran crabs

The complete mitochondrial genome (mitogenome) sequences of two primitive crabs, Umalia orientalis and Lyreidus brevifrons (Decapoda: Brachyura: Raninidae) were determined. The mitogenomes of the two species are 15,466 and 16,112bp in length with AT content of 68.0% and 70.6%, respectively. Each genome contains 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes. The gene arrangement of U. orientalis is the same with those reported for most brachyuran species. Nevertheless, the gene arrangement of L. brevifrons differs from that of U. orientalis in having an additional non-coding region. The newly found non-coding region is located between nad3 and trnA with 641bp in length. Its nucleotide composition and secondary structure are similar to the typical control region. In L. brevifrons, the secondary structures of trnS-AGN and trnI are significantly different from those in U. orientalis and other brachyuran species. The start codon for cox1 is ATG in all reported Eubrachyura mitogenomes, while a common start codon ACG is found in the Podotremata. Phylogenetic analyses for crustacean decapods based on the nucleotide and amino acid of 13 PCGs indicate that Homolidae is more primitive in Brachyura, and Raninidae is a sister group to Eubrachyura. This implies that Raninidae is closer to Eubrachyura than to Homolidae, and Podotremata may be a paraphyletic assemblage. The results also indicate that the subfamily Lyreidinae is closer to Notopodinae than to Ranininae within Raninidae. The novel mitogenome data provides useful information for refining the phylogenetic relationships within Brachyura.

Species radiation by DNA replication that systematically exchanges nucleotides?

RNA and DNA syntheses share many properties. Therefore, the existence of 'swinger' RNAs, presumed 'orphan' transcripts matching genomic sequences only if transcription systematically exchanged nucleotides, suggests replication producing swinger DNA. Transcripts occur in many short-lived copies, the few cellular DNA molecules are long-lived. Hence pressures for functional swinger DNAs are greater than for swinger RNAs. Protein coding properties of swinger sequences differ from original sequences, suggesting rarity of corresponding swinger DNA. For genes producing structural RNAs, such as tRNAs and rRNAs, three exchanges (A<->T, C<->G and A<->T+C<->G) conserve self-hybridization properties. All nuclear eukaryote swinger DNA sequences detected in GenBank are for rRNA genes assuming A<->T+C<->G exchanges. In brachyuran crabs, 25 species had A<->T+C<->G swinger 18S rDNA, all matching the reverse-exchanged version of regular 18S rDNA of a related species. In this taxon, swinger replication of 18S rDNA apparently associated with, or even resulted in species radiation. A<->T+C<->G transformation doesn't invert sequence direction, differing from inverted repeats. Swinger repeats (detectable only assuming swinger transformations, A<->T+C<->G swinger repeats most frequent) within regular human rRNAs, independently confirm swinger polymerizations for most swinger types. Swinger replication might be an unsuspected molecular mechanism for ultrafast speciation.

The complete mitochondrial genome of red frog crab Ranina ranina (Crustacea: Decapoda: Brachyura: Raninidae)

Although the brachyuran nature of Raninoidea is widely accepted, there is no consensus over the precise position of the Raninoidea within Brachyura. Long PCR and primer walking methods are employed to determine the first complete mitochondrial genome (mitogenome) sequence of raninoidian crab, Ranina ranina. It is a circular double-stranded DNA molecule of 15,563 base pairs (bp) in length with a standard set of 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs) as well as a putative non-coding control region. The gene order is substantially consistent with that of the pancrustacean ground pattern with the tRNA(His) gene rearrangement. The basal placement of R. ranina in the phylogenetic tree integrated with a similar genomic organization to ancestral pancrustacea confirmed the primitive position of R. ranina in the Brachyura.

Cloning, expression, characterization and phylogenetic analysis of arginine kinase from greasyback shrimp (Metapenaeus ensis)

Arginine kinase (AK) plays an important role in cellular energy metabolism in invertebrate. The encoding AK gene from Shrimp Metapenaeus ensis (M. ensis) was cloned in prokaryotic expression plasmid pET-28a, and it was then expressed in Escherichia coil in dissoluble form. The recombinant protein was purified by following three chromatography steps in turn: CM-Cellulose cation-exchange, Sephacryl S-100HR gel filtrate and DEAE-Sepharose anion-exchange. The purified AK's apparent K(m) was 2.33+/-0.1 and 1.59+/-0.2 mM for ATP and l-arginine, respectively, while its optimum pH and temperature was 8.5 and 30 degrees C in the process of forward reaction, respectively. Phylogenetic analysis of cDNA-derived amino acid sequences for the AKs indicated a close affinity of M. ensis and another shrimp (Litopenaeus vannamei).