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

Pangenomes at the limits of evolution

Evolutionary pathways can be random or deterministic. In a recent article, Beavan et al. investigate this balance by applying machine learning models to microbial pangenomes. The presence of almost one-third of genes can be reliably inferred, indicating a surprising amount of predictable evolution.

Morphological diversity in true and false crabs reveals the plesiomorphy of the megalopa phase

Brachyura and Anomala (or Anomura), also referred to as true and false crabs, form the species-rich and globally abundant group of Meiura, an ingroup of Decapoda. The evolutionary success of both groups is sometimes attributed to the process of carcinization (evolving a crab-like body), but might also be connected to the megalopa, a specific transitional larval phase. We investigate these questions, using outline analysis of the shields (carapaces) of more than 1500 meiuran crabs. We compare the morphological diversity of different developmental phases of major ingroups of true and false crabs. We find that morphological diversity of adults is larger in false crabs than in true crabs, indicating that taxonomic diversity and morphological diversity are not necessarily linked. The increasing morphological disparity of adults of true and false crabs with increasing phylogenetic distance furthermore indicates diverging evolution of the shield morphology of adult representatives of Meiura. Larvae of true crabs also show larger diversity than their adult counterparts, highlighting the importance of larvae for biodiversity studies. The megalopa phase of Meiura appears to be plesiomorphic, as it overlaps between true and false crabs and shows little diversity. Causes may be common evolutionary constraints on a developmental phase specialized for transitioning.

Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae)

Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.

Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome

Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.

Demographic changes and life-history strategies predict the genetic diversity in crabs

Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analysed across 150 species (16 992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.

Optimal planar leg geometry in robots and crabs for idealized rocky terrain

Natural terrain is uneven so it may be beneficial to grasp onto the depressions or 'valleys' between obstacles when walking over such a surface. To examine how leg geometry influences walking across obstacles with valleys, we (1) modeled the performance of a two-linkage leg with parallel axis 'hip' and 'knee' joints to determine how relative segment lengths influence stepping across rocks of varying diameter, and (2) measured the walking limbs in two species of intertidal crabs,Hemigrapsus nudusandPachygrapsus crassipes, which live on rocky shores and granular terrains. We idealized uneven terrains as adjacent rigid hemispherical 'rocks' with valleys between them and calculated kinematic factors such as workspace, limb angles with respect to the ground, and body configurations needed to step over rocks. We first find that the simulated foot tip radius relative to the rock radius is limited by friction and material failure. To enable force closure for grasping, and assuming that friction coefficients above 0.5 are unrealistic, the foot tip radius must be at least 10 times smaller than that of the rocks. However, ratios above 15 are at risk of fracture. Second, we find the theoretical optimal leg geometry for robots is, with the distal segment 0.63 of the total length, which enables the traversal of rocks with a diameter that is 37% of the total leg length. Surprisingly, the intertidal crabs' walking limbs cluster around the same limb ratio of 0.63, showing deviations for limbs less specialized for walking. Our results can be applied broadly when designing segment lengths and foot shapes for legged robots on uneven terrain, as demonstrated here using a hexapod crab-inspired robot. Furthermore, these findings can inform our understanding of the evolutionary patterns in leg anatomy associated with adapting to rocky terrain.

Evolvability in the Cephalothoracic Structural Complexity of Aegla araucaniensis (Crustacea: Decapoda) Determined by a Developmental System with Low Covariational Constraint

Simple Summary

The origin of complex morphological structures is explained mainly by direct pathways fusing adjacent modules, while the independent effect of parallel pathways acting on different areas of a morphogenetic field is less well-known. The palimpsest model that explains the cephalothoracic structural complexity of decapod crustaceans is composed of two hox-regulatory parallel pathways that tagmatize the anterior metameres early, followed by a direct pathway that fuses the tagmata forming the developmental modules. The cephalothoracic geometry of Aegla araucaniensis shows a marked sexual dimorphism; its adaptive causes also promote dimorphic variations in the evolvability of developmental modularity. We found areas of instability in the variance of the asymmetry in both developmental modules. The direct pathway presents intermediate levels of canalization in the covariation of the developmental modules, although significantly higher in males. This low restrictive potential promotes expressions of gonadic modularity in females and agonistic modularity in males, which differ significantly from developmental modularity. The cephalothoracic palimpsest model of decapods allows studying modularity in an explicit evo–devo context.

Abstract

The integration of complex structures is proportional to the intensity of the structural fusion; its consequences are better known than the covariational effects under less restrictive mechanisms. The synthesis of a palimpsest model based on two early parallel pathways and a later direct pathway explains the cephalothoracic complexity of decapod crustaceans. Using this model, we tested the evolvability of the developmental modularity in Aegla araucaniensis, an anomuran crab with an evident adaptive sexual dimorphism. The asymmetric patterns found on the landmark configurations suggest independent perturbations of the parallel pathways in each module and a stable asymmetry variance near the fusion by canalization of the direct pathway, which was more intense in males. The greater covariational flexibility imposed by the parallel pathways promotes the expression of gonadic modularity that favors the reproductive output in females and agonistic modularity that contributes to mating success in males. Under these divergent expressions of evolvability, the smaller difference between developmental modularity and agonistic modularity in males suggests higher levels of canalization due to a relatively more intense structural fusion. We conclude that: (1) the cephalothorax of A. araucaniensis is an evolvable structure, where parallel pathways promote sexual disruptions in the expressions of functional modularity, which are more restricted in males, and (2) the cephalothoracic palimpsest of decapods has empirical advantages in studying the developmental causes of evolution of complex structures.

The remarkable visual system of a Cretaceous crab

True crabs (Brachyura) are one of the few groups of arthropods to evolve several types of compound eye, the origins and early evolution of which are obscure. Here, we describe details of the eyes of the Cretaceous brachyuran Callichimaera perplexa, which possessed remarkably large eyes and a highly disparate body form among brachyurans. The eyes of C. perplexa preserve internal optic neuropils and external corneal elements, and it is the first known post-Paleozoic arthropod to preserve both. Additionally, a series of specimens of C. perplexa preserve both the eyes and carapace, allowing for the calculation of the optical growth rate. C. perplexa shows the fastest optical growth rate compared with a sample of 14 species of extant brachyurans. The growth series of C. perplexa, in combination with the calculation of the interommatidial angle and eye parameter, demonstrates that it was a highly visual predator that inhabited well-lit environments.

•

We report optical details of the Cretaceous brachyuran crab Callichimaera perplexa

•

It preserves both internal optic neuropils and external corneal elements

•

Callichimaera has a faster optical growth rate than a series of extant crabs

•

Callichimaera was a highly visual predator inhabiting well-lit environments

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.