A comprehensive molecular phylogeny of the brachyuran crab superfamily Xanthoidea provides novel insights into its systematics and evolutionary history

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.

Shift in symbiotic lifestyle as the major process shaping the evolution of pea crabs (Decapoda: Brachyura: Pinnotheroidea)

The pea crabs, superfamily Pinnotheroidea, are exceptional among brachyuran crabs in their diverse symbiotic associations involving both inquilinism and protective symbiosis. While this group presents a rare opportunity for evolutionary comparative study of host switching and morphological evolution in marine macroinvertebrates, previous phylogenetic studies have been focused on systematics. Here, we reconstructed the most extensive phylogeny of Pinnotheroidea based on two mitochondrial and six nuclear markers, with the aim of elucidating the host switching pathways and the correlation between symbiotic lifestyles and selected morphological adaptations. Ancestral state reconstruction of host association revealed a monophyletic origin of symbiosis in the form of inquilinism. Subsequent shifts in microhabitat preference for burrows or worm tubes, and the move to protective symbiosis, primarily in the switch to mollusc endosymbiosis, contributed to radiation in Pinnotheridae. Further parallel colonisations of echinoderms and tunicates occurred but did not lead to extensive diversification, except in the Clypeasterophilus + Dissodactylus lineage, which experienced a unique switch to echinoderm ectosymbiosis. The evolution of the third maxillipeds, carapace shape and ambulatory pereiopods suggests a rather strong coupling with the symbiotic lifestyle (whether inquilinism or protective symbiosis). Phenotypic diversity of these characters was higher among species engaged in protective symbiosis, with convergence in form (or function) among those sharing the same host affiliation. Species having different host affiliations or symbiotic lifestyles might also exhibit convergence in the form of the three morphological traits, suggesting a common adaptive value of the specialisations. Pinnotherid crabs overall exhibited a lower trait diversity than the also symbiotic palaemonid shrimps with comparable species diversity. This may plausibly be attributed to differences in potential for morphological modification to serve additional functions among the traits analysed in the two groups, the less frequent host switching and the less diverse host affiliations, and thus a less complicated evolutionary history in pinnotherids.

On the systematic placement of the fossil crab Lathahypossia aculeata (Busulini, Tessier & Visentin, 1984) (Crustacea: Decapoda: Brachyura)

The systematic placement of the iconic fossil crab, Lathahypossia aculeata (Busulini, Tessier & Visentin, 1984) (formerly in Titanocarcinus A. Milne-Edwards, 1864), from the Eocene of Italy is revised. The examination of two specimens that had the ventral and subcephalic features well preserved has allowed us to better understand the morphology of this species. As a result, Lathahypossia aculeata must be removed from the Hypothalassiidae (Eriphioidea), where it is now placed, and moved to the Xanthidae (Xanthoidea). The present work again highlights the importance of ventral characters in the study of fossil crabs and allows a more accurate systematic classification.

Allopatric mosaics in the Indo-West Pacific crab subfamily Chlorodiellinae reveal correlated patterns of sympatry, genetic divergence, and genitalic disparity

Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry. We present a phylogeny of the crab subfamily Chlorodiellinae which displays allopatric mosaics within species. These allopatric lineages typically do not have divergent male genitalia, while older sympatric lineages do. We tested the relationship between genetic distance (proxy for time), sympatry, and the divergence of male genitalic morphology. Our results suggest that male genitalic divergence is not involved in the initiation of speciation in chlorodielline crabs, having likely occurred only after isolation began in allopatry. However, morphological evolution of genitalia seemingly does play an important role in completing the process of speciation in these crabs.