Molecular phylogeny of the brachyuran crab superfamily Majoidea indicates close congruence with trees based on larval morphology

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.].

Ecology determines appearance: a new taxonomic solution for the soft bottom dwelling spider crab Pisoides bidentatus (A. Milne-Edwards, 1873) from the Sea of Japan, with remarks on Pisoides ortmanni (Balss, 1924) and the northwestern Pacific Pugettia Dana, 1851 (Majoidea: Epialtidae)

The northwestern Pacific soft bottom dwelling spider crab, Pisoides bidentatus (A. Milne-Edwards, 1873) (Brachyura: Majoidea: Epialtidae), is re-described using an integrative approach. As a result, it is transferred to the genus Scyra Dana, 1851 (Epialtidae) based on morphological and molecular data, as well as already described larval morphology, which certainly better reflects the phylogenetic relationships of the species. Japanese Pisoides ortmanni (Balss, 1924), for which morphology and ecology are very similar to P. bidentatus as well as Pugettia quadridens (De Haan, 1839) and the closely related Pugettia ferox Ohtsuchi & Kawamura, 2019, are also transferred to Scyra. The "reduced" morphology of both species is very different from the related northwestern Pacific Scyra spp. and Pugettia spp., which are mostly decorating algae-dwellers. We associate the relatively long ambulatory legs, a smooth tear-drop shaped carapace with a reduced dorsal armature and slightly pronounced pseudorostral spines, characteristic of P. bidentatus and P. ortmanni with their open soft (mainly sand) bottom habitats, where it is difficult to find a foothold or shelter, but it is necessary to resist constant currents. Such morphology is also characteristic of spider crabs of the genera Libinia Leach, 1815 and Doclea Leach, 1815 (Epialtidae: Pisinae), which are also living in similar habitats/conditions and represent a convergent morphological appearance.

The complete mitochondrial genome of Scyra compressipes Stimpson, 1857 (Decapoda: Epialtidae)

The family Epialtidae is the most diversified family within superfamily Majoidea but there is no report for complete mitogenome of any species in this family. This study was performed to sequence a complete mitogenome of Scyra compressipes Stimpson, 1857, as the first mitochondrial genome report from the Epialtidae. The complete mitogenome sequence of S. compressipes was 16,415 bp and it consisted of 36 genes, including 13 protein-coding genes (PCGs), two rRNA genes, and 21 tRNA genes excluding tRNA-Leu (UAG). tRNA genes ranged from 63 bp to 72 bp in length. The base composition of a complete mitogenome of S. compressipes is 34.7% A, 15.3% C, 10.2% G, and 39.8% T. The phylogenetic position of S. compressipes in the superfamily Majoidea was examined based on 13 PCGs. The phylogenetic analysis showed that S. compressipes was most closely related to Maguimithrax spinosissimus, a representative of the family Mithracidae.

Insights into the evolution of Brachyura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements

Brachyura is one of the most species rich and highly derived groups among extant crustaceans, with over 7250 known species. However, brachyuran phylogeny remains controversial and requires further study. Here, we combined 103 brachyuran mitogenomes from GenBank with 10 new mitogenomes to describe gene rearrangement patterns and explore the internal phylogenetic relationships of Brachyura. Most of the 10 novel mitogenomes had the typical 37 genes, except that of Longpotamon depressum, which lacked trnQ. We discovered 15 gene rearrangement patterns among Brachyura and preliminarily determined their rearrangement mechanisms with the help of CREx. We identified seven putative ancestral family gene orders among the 15 rearrangement patterns and expounded systematically upon the mechanisms of their rearrangement. In our phylogenetic analysis, Raninoida shared a sister relationship with an eubrachyuran clade ((Heterotremata [Potamoidea] + Thoracotremata) + Heterotremata) at maximum nodal support rather than Dromiacea, which did not support monophyly of Podotremata. In addition, Potamoidea (Parathelphusidae + Potamidae) retained a close relationship with Thoracotremata rather than their marine relatives in Heterotremata. Our study provides important information for the evolution of Brachyura by using the large taxon sampling currently available for systematic rearrangement and phylogenetic analyses.

A molecular perspective on the systematics of the spider crab genus Libinia Leach, 1815 (Majoidea:Epialtidae)

Libinia, a genus of spider crabs, encompasses 10 valid species, three from the eastern Pacific and seven from the western Atlantic. Previous phylogenetic hypotheses based on molecular and larval morphological data suggested an uncertain position of the genus Libinia within the family Epialtidae. Therefore, we investigated the evolutionary relationships among the species of Libinia, and also suggested a position for this genus within the family. Phylogenetic trees were obtained from concatenated mtDNA sequences of 16S and COI fragments. Molecular dating methods were used to estimate the relative timing of origin and diversification within Libinia. Eighteen new primers were designed, and PCR conditions were standardised to amplify the COI fragments of older or poorly preserved pinned specimens, generating ~550 base pair sequences. Phylogenetic hypotheses supported the monophyly of the genus. Species that occur in the eastern Pacific and the ones found in the western Atlantic do not form monophyletic clades related to this geographical separation. In the eastern Pacific, there is low phylogenetic proximity between Libinia mexicana and L. setosa; and since we did not sample L. peruana, we inferred that it should cluster with L. setosa or L. mexicana due to morphological similarity. Libinia spinosa is separate from the other species, L. mexicana was a sister group of L. cavirostris, and L. ferreirae was closely related to L. dubia and L. rhomboidea, which occur in the Gulf of Mexico and in the Caribbean, respectively. In the Gulf of Mexico, L. dubia and L. emarginata are closely related. Although L. erinacea was not sampled, we suggest, from previous studies, that it should group with L. dubia due to morphological similarities. The phylogenetic hypothesis suggests the monophyly of Libinia, with its origins at the late Eocene. Finally, the recovered clades based on two molecular markers agreed with a parallel, linked morphological study that is still in progress.

A new genus for Pericera septemspinosa Stimpson, 1871 and Pericera heptacantha Bell, 1836 (Crustacea, Brachyura, Majoidea), based on morphology and molecular data

A new genus of majoid spider crab, Pohleusgen. nov. is established for Pericera septemspinosa Stimpson, 1871 and Pericera heptacantha Bell, 1836, based on morphology and molecular data from the partial sequences of the 12S and 16S mitochondrial genes and the 18S small subunit rRNA nuclear locus. The species are re-described and illustrated, based on material from several localities of the western Atlantic and eastern Pacific oceans. The carapace, antennal and pterygostomial spines, male thoracic sternum and first gonopods are distinctive characters, distinguishing Pohleusgen. nov. from species assigned to Macrocoeloma Miers, 1879, where P. septemspinosus and P. heptacanthus are currently included.

Varying colour pattern, yet genetically similar: Pebble Crab Seulocia vittata (Stimpson, 1858) (Brachyura: Leucosiidae) from the southeastern coast of India

Five adult specimens of leucosiid crab Seulocia vittata (Stimpson, 1858) were recently collected off the coast of Palk Bay, southern India.  Typical morphological examination revealed the presence of two colour patterns: grey and red.  Interestingly, molecular analysis based on the barcoding gene cytochrome oxidase sub unit I (COI) revealed that both grey and red colour patterns in S. vittata showed 0% sequence divergence between the specimens.  This indicates a situation of reverse cryptic behavior in this crab.  Surprisingly, the evolutionary and ecological processes leading to the absence of genetic divergence and variation in morphology (colour pattern) in S. vittata complex remain to be addressed.   

A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

Three new species and a new genus of majoid crabs from the eastern Pacific (Decapoda, Brachyura)

Three new species and a new genus of majoid crabs from deep waters in the eastern Pacific are described and illustrated using morphological and molecular data. A new species of inachoidid, Collodesanartius sp. n. is described from Peru, which resembles C.tenuirostris Rathbun, 1893, in the general appearance of the carapace, but is distinguished by the details of tubercles on the carapace and thoracic sternum, proportions of the pereopod articles, and bathymetric distribution. A new epialtid, Nibiliamachala sp. n., is described from Ecuador; Nibilia A Milne-Edwards, 1878 has, until now, been considered to be monotypic, occurring only in the western Atlantic. This new species, from the eastern Pacific, closely resembles N.antilocapra (Stimpson, 1871) in the general morphology, but can be distinguished by the number of spines on the carapace and pereopods. Another epialtid, Solincaaulix gen. n. et sp. n, is establish for material collected from Ecuador and Peru, and can be easily identified from other taxa by the presence of a deep furrow between the very inflated branchial regions.

The snapping shrimp dactyl plunger: a thermomechanical damage-tolerant sandwich composite

The dactyl plunger of Alpheus sp. was found to be a layered composite, with mineral-rich outer and inner layers and a chitin-rich middle layer of high porosity. The chitin-rich middle layer is itself composed of several porous chitin laminae. Modelling heat conduction through the plunger cross-section revealed that the chitin-rich layer is able to insulate heat and retard its progress through the material. Heat accumulates in the plunger after a series of successive snaps and as such, its thermally resistant design can be considered most useful under the conditions of successive snapping. The plunger has a concurrent mechanical damage-tolerant design with biogenic mineral layers, viscous (chitin-mineral) interfaces, energy-dissipating porous chitin, and sidewalls composed of ordered, layered aragonite. The snapping shrimp plunger has a design that may protect it and internal soft tissues from thermomechanical damage during plunger-socket compression prior to cavitation bubble release.

Ultrastructure of spermatozoa of spider crabs, family Mithracidae (Crustacea, Decapoda, Brachyura): Integrative analyses based on morphological and molecular data

Recent studies based on morphological and molecular data provide a new perspective concerning taxonomic aspects of the brachyuran family Mithracidae. These studies proposed a series of nominal changes and indicated that the family is actually represented by a different number and representatives of genera than previously thought. Here, we provide a comparative description of the ultrastructure of spermatozoa and spermatophores of some species of Mithracidae in a phylogenetic context. The ultrastructure of the spermatozoa and spermatophore was observed by scanning and transmission electron microscopy. The most informative morphological characters analysed were thickness of the operculum, shape of the perforatorial chamber and shape and thickness of the inner acrosomal zone. As a framework, we used a topology based on a phylogenetic analysis using mitochondrial data obtained here and from previous studies. Our results indicate that closely related species share a series of morphological characteristics of the spermatozoa. A thick operculum, for example, is a feature observed in species of the genera Amphithrax, Teleophrys, and Omalacantha in contrast to the slender operculum observed in Mithraculus and Mithrax. Amphithrax and Teleophrys have a rhomboid perforatorial chamber, while Mithraculus, Mithrax, and Omalacantha show a wider, deltoid morphology. Furthermore, our results are in agreement with recently proposed taxonomic changes including the separation of the genera Mithrax (previously Damithrax), Amphithrax (previously Mithrax) and Mithraculus, and the synonymy of Mithrax caribbaeus with Mithrax hispidus. Overall, the spermiotaxonomy of these species of Mithracidae represent a novel set of data that corroborates the most recent taxonomic revision of the family and can be used in future taxonomic and phylogenetic studies within this family.

DNA sequence database as a tool to identify decapod crustaceans on the São Paulo coastline

DNA barcoding has emerged as an efficient tool for taxonomy and other biodiversity fields. The vast and speciose group of decapod crustaceans is not an exception in the current scenario and comparing short DNA fragments has enabled researchers to overcome some taxonomic impediments to help broadening knowledge on the diversity of this group of crustaceans. Brazil is considered as an important area in terms of global marine biodiversity and some regions stand out in terms of decapod fauna, such as the São Paulo coastline. Thus, the aim of this study is to obtain sequences of the mitochondrial markers (COI and 16S) for decapod crustaceans distributed at the São Paulo coastline and to test the accuracy of these markers for species identification from this region by comparing our sequences to those already present in the GenBank database. We sampled along almost the 300 km of the São Paulo coastline from estuaries to offshore islands during the development of a multidisciplinary research project that took place for 5 years. All the species were processed to obtain the DNA sequences. The diversity of the decapod fauna on the São Paulo coastline comprises at least 404 species. We were able to collect 256 of those species and sequence of at least one of the target genes from 221. By testing the accuracy of these two DNA markers as a tool for identification, we were able to check our own identifications, including new records in GenBank, spot potential mistakes in GenBank, and detect potential new species.

Carapace surface architecture facilitates camouflage of the decorator crab Tiarinia cornigera

This paper elucidates the unique setal morphology of the decorator crab Tiarinia cornigera, and further presents evidence to that setal morphology promotes micro-organism nucleation and adhesion. The carapace of this crab is covered by clusters of setae, each comprising a hollow acicular stem that is enveloped by a haystack-like structure. Using computational fluid dynamics, we find that these setae are responsible for manipulating water flow over the carapace surface. Micro-organisms in the sea water, nest in areas of flow stagnation and as a result, nucleate to and biofoul the setae by means of chemical adhesion. Attached micro-organisms secrete extracellular polymeric substances, which we deduce must also provide an additional element of chemical adhesion to mechanically interlocked mesoscopic and macroscopic biomatter. By coupling physical and chemical methods for adhesion, T. cornigera is able to hierarchically decorate its carapace.

STATEMENT OF SIGNIFICANCE

Our paper brings to light the unique decorator crab carapace morphology of T. cornigera; and furthermore evidences its function in micro-organism nucleation and adhesion. We show how this special carapace morphology directs and guides water flow to form nesting regions of water stagnation where micro-organisms can nucleate and adhere. In the literature, decorator crab carapaces are presumed to be able to mechanically interlock biomatter as camouflage using hook-like setal outgrowths. T. cornigera contrarily exhibits clusters of hay-stack like structures. By encouraging micro-organism adhesion to the carapace setae, T. cornigera is able to effectively attach biomatter using both chemical and physical principles of adhesion. T. cornigera essentially has a super-biofouling carapace surface, for at least micro-organisms. Our work will have an impact on researchers interested in biofouling, adhesion, biomedical and purification filter systems, and in the development of novel biomimetic surfaces with tailored properties.

Taxonomic and Biogeographical Status of Three Species of the Spider Crabs of the Genus Acanthonyx Latreille, 1828 (Majoidea: Epialtidae) as Determined by DNA Barcoding and Morphological Analyses Along the Western Atlantic

Ana Francisca Tamburus and Fernando Luis Mantelatto (2016) The genus Acanthonyx Latreille, 1828 contains 17 valid species, including A. dissimulatus Coelho, 1993, A. petiverii H. Milne Edwards, 1834 and A. scutiformis (Dana, 1851), which occur along the Brazilian coast. The high degree of intraspecific variation in the angle of hepatic region, size of the tubercles of the carapace and length of setae on the carapace and pereopods has resulted in difficulties with the taxonomy of this genus. Analysis of more consistent morphological and molecular characters are required to clarify the status of the three species that occurs in Brazil. For the molecular data, we used the barcode region of the mitochondrial gene COI as a marker, and we correlated this with morphological characters of adults and juveniles. The three species of Acanthonyx were morphologically similar and the matrix of genetic distances and maximum likelihood trees showed that A. dissimulatus and A. scutiformis belonged to the same group with A. petiverii. They could not be separated using the diagnosing characters proposed in the original description or genetically (present study), thus indicating that the taxonomic status of the first two species is questionable. The division into two distinct groups corresponding to A (Caribbean, Brazil, Venezuela) and B (USA, Mexico) was well supported and indicated that there are genetic differences between these populations. Present study suggests the existence of a single species in Brazil and Caribbean, assigned to A. petiverii (type locality in Antilles). The existence of a new species restricted to North America confirms the cryptic diversity within Acanthonyx.

Porcelain crabs of the genera Pachycheles Stimpson and Neopisosoma Haig (Decapoda : Anomura : Porcellanidae): new premises based on molecular data and comments on phylogenetic relationships in the family

Porcellanidae Haworth, 1825 is a family of marine anomuran crabs distributed throughout tropical and temperate regions of all the oceans, typically littoral and sublittoral waters, with a considerable diversity of lifestyles, habitats and colouration. Pachycheles Stimpson, 1858 and Neopisosoma Haig, 1960 share, among other morphological characteristics, the fragmentation of the lateral carapace walls. The morphology of this body region was key to supporting the establishment of Neopisosoma, which increased uncertainty about the taxonomic status of these genera due to the high intraspecific variation of this character. Our study reconstructs the phylogenetic relationship between Pachycheles and Neopisosoma based on mitochondrial and nuclear DNA sequences to evaluate whether these are valid taxa. While Pachycheles seems to be monophyletic, the position of Neopisosoma mexicanum (Streets, 1871) indicates that the group is polyphyletic, and deserves further investigation. Pachycheles is revealed to be older than Neopisosoma, and likely originated in the Indo-Pacific, later spreading to the American continent during the early Tertiary. Neopisosoma may have arisen much later in the Caribbean Province before the closure of the Isthmus of Panama, explaining its distribution, which is restricted mainly to Central America. The inclusion of a considerable number of species from both genera represents a significant advance in the study of this controversial group. The phylogenetic reconstruction of Pachycheles unveiled clades corroborated by morphology, but also revealed unclear relationships, which may indicate the potential existence of cryptic species.

Molecular phylogenetics and taxonomic reanalysis of the family Mithracidae MacLeay (Decapoda : Brachyura : Majoidea)

Mithracid crabs comprise a primarily subtidal reef- and rubble-dwelling group inhabiting both tropical and subtropical seas. Despite their relative ubiquity in many hard-substrate environments, there has been little consensus about their phylogenetic relationships or whether their group rank should be that of subfamily or family. We have used a combined molecular dataset of two nuclear (18S, H3) and three mitochondrial (12S, 16S, COI) genes to build a preliminary molecular phylogeny of Majoidea in order to examine the membership of Mithracidae. We then built a second molecular phylogeny based on three mitochondrial genes to assess the internal composition of the family, and conducted comparative morphological examinations of genera and species that resolved in unexpected positions on the phylogram. Four genera are designated under new or resurrected names on the basis of molecular and morphological characters, while memberships of several other existing genera are modified. Following review of molecular and morphological characters, the genera Coelocerus, Cyclocoeloma, Cyphocarcinus, Leptopisa, Micippa, Picrocerodes, Stenocionops and Tiarinia are provisionally excluded from Mithracidae s.s., while Hemus and Pitho are included in it. A key to genera of Mithracidae is provided.

DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach

Marine crustaceans are known as a group with a high level of morphological and ecological diversity but are difficult to identify by traditional approaches and usually require the help of highly trained taxonomists. A faster identification method, DNA barcoding, was found to be an effective tool for species identification in many metazoan groups including some crustaceans. Here we expand the DNA barcode database with a case study involving 80 malacostracan species from the Estuary and Gulf of St Lawrence. DNA sequences for 460 specimens grouped into clusters corresponding to known morphological species in 95% of cases. Genetic distances between species were on average 25 times higher than within species. Intraspecific divergence was high (3.78-13.6%) in specimens belonging to four morphological species, suggesting the occurrence of cryptic species. Moreover, we detected the presence of an invasive amphipod species in the St Lawrence Estuary. This study reconfirms the usefulness of DNA barcoding for the identification of marine crustaceans.

Systematic and evolutionary insights derived from mtDNA COI barcode diversity in the Decapoda (Crustacea: Malacostraca)

BACKGROUND

Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world.

METHODOLOGY/PRINCIPAL FINDINGS

We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content.

CONCLUSIONS/SIGNIFICANCE

Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.