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Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of the group. Here, we reconstruct the most comprehensive phylogeny of Brachyura to date using sequence data of six nuclear protein-coding genes and two mitochondrial rRNA genes from more than 140 species belonging to 58 families. The gene tree confirms that the “Podotremata,” are paraphyletic. Within the monophyletic Eubrachyura, the reciprocal monophyly of the two subsections, Heterotremata and Thoracotremata, is supported. Monophyly of many superfamilies, however, is not recovered, indicating the prevalence of morphological convergence and the need for further taxonomic studies. Freshwater crabs were derived early in the evolution of Eubrachyura and are shown to have at least two independent origins. Bayesian relaxed molecular methods estimate that freshwater crabs separated from their closest marine sister taxa ∼135 Ma, that is, after the break up of Pangaea (∼200 Ma) and that a Gondwanan origin of these freshwater representatives is untenable. Most extant families and superfamilies arose during the late Cretaceous and early Tertiary.

Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensive taxonomic sampling of any freshwater crab family globally, and explores the impact of paleodrainage interconnectivity on cladogenesis among freshwater crabs. Phylogenetic analyses of the total evidence data using maximum-likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) produced a robust statistically well-supported tree topology that reaffirmed the monophyly of the Afrotropical freshwater crab fauna. The estimated divergence times suggest that the Afrotropical Potamonautidae diverged during the Eocene. Cladogenesis within and among several genera occurred predominantly during the Miocene, which was associated with major tectonic and climatic ameliorations throughout the region. Paleodrainage connectivity was observed with specimens from the Nilo-Sudan and East African coast proving to be sister to specimens from the Upper Guinea Forests in West Africa. In addition, we observed strong sister taxon affinity between specimens from East Africa and the Congo basin, including specimens from Lake Tanganyika, while the southern African fauna was retrieved as sister to the Angolan taxa. Within the East African clade we observed two independent transoceanic dispersal events, one to the Seychelles Archipelago and a second to Madagascar, while we observe a single transoceanic dispersal event from West Africa to Sao Tomé. The ancestral area estimation suggested a West African/East African ancestral range for the family with multiple dispersal events between southern Africa and East Africa, and between East Africa and Central Africa The taxonomic implications of our results are discussed in light of the widespread paraphyly evident among a number of genera.

Background The Sox (SRY-related HMG-box) transcription factor family plays central roles in cell fate determination, neurogenesis, and reproductive development, yet its evolutionary history and molecular diversification in crustaceans remain poorly understood. Here we present a genome-wide comparative study of Sox genes in three representative crabs— Portunus trituberculatus , Scylla paramamosain , and Eriocheir sinensis —based on their high-quality reference genomes. Results We identified 16, 16, and 15 Sox genes, respectively, and established a robust HMG-box–based phylogeny and nomenclature, assigning all members to the canonical B–F subgroups and an ungrouped Sox-like clade. Comparative analyses uncovered striking lineage-specific events, including the complete loss of SoxB1 in E. sinensis and an expansion of the SoxC subgroup, accompanied by a mosaic of deeply conserved and newly derived motifs and domains. Integrative transcriptomic analyses revealed that many Sox genes are strongly expressed in neural tissues and testes, and that certain SoxB and SoxC members exhibit stage-specific activation during embryonic, larval, or testicular development, highlighting key roles in neurogenesis, pluripotency maintenance, and spermatogenesis. Conclusions Together, these findings provide the first comprehensive evolutionary framework for the crab Sox family, uncover unexpected gene loss and subgroup expansion, and offer new insights into how conserved transcriptional regulators diversify to shape neural and reproductive programs in arthropods.

Two new complete mitogenomes of the grapsids, Metaplax longipes Stimpson, 1858 and Nanosesarma minutum (De Man, 1887) were sequenced using next-generation sequencing (NGS). By analyzing a combination of 75 Brachyura taxa, our phylomitogenomic inferences suggested that Metaplax crab seperated earlier from the sesarmid crabs and closely related to the varunids with respect to Nanosesarma crab. It reconfirmed that the Metaplax should be removed from the Sesarmidae and assinged to the Varunidae. Additional mitogenomic comparisons including gene rearrangement and genomic organization were conducted among the 33 taxa of Grapsoidea and Ocypodoidea, and a shared rearrangement pattern between Metaplax longipes and the varunids were recovered, which also strongly supported the inference for the phylogenetic position of the Metaplax.

Chinese mitten crab ( Eriocheir Sinensis ) is a commercially important species in Chinese aquaculture, yet the genetic structure of wild populations remains poorly understood. A total of 240 wild E. sinensis samples were collected from Liaohe (LH), Yalujiang (YLJ), Huanghe (HH), Yangtze (including Anqing section (YZA), Taixing section (YZT)), Oujiang (OJ), Minjiang (MJ), and Beilunhe (BLH) River basins to investigate the genetic structure of native populations. Through genotyping-by-sequencing (GBS) and stringent quality filtering, a total of 3,120,408 high-quality single- nucleotide polymorphism (SNP) loci were identified. Principal component analysis (PCA) showed that the BLH and MJ populations formed distinct clusters, whereas OJ, YZA, YZT, HH, LH, and YLJ populations were loosely clustered. Phylogenetic tree and population genetic structure analyses revealed that the BLH River population in southern China was the only significantly differentiated group within the native range of the Chinese mitten crab, while northern populations (HH, LH, and YLJ) exhibited stronger admixture, indicating higher levels of gene flow. Additionally, gene flow occurred more frequently among geographically proximate populations, while weaker gene flow persisted between geographically distant groups. Further selective sweep analyses comparing representative southern and northern populations (BLH and LH) identified key genes under strong geographic selection, primarily involved in transcriptional regulation, metabolism and transport, stress response and damage repair, and signal transduction. Overall, this study provides comprehensive insights into the genetic resources of wild E. sinensis across Chinese river basins, laying a foundation for conservation and germplasm resource development. Highlights λ Genome-wide SNP markers were developed to systematically characterize genetic diversity and population structure of wild Eriocheir sinensis across seven major river basins. λ The Beilunhe River population was identified as the only significantly differentiated genetic unit. λ No significant genetic differentiation was found among the northern E. sinensis populations from the Yalujiang, Huanghe and Liaohe Rivers.

Salinity is the primary driver of osmoregulatory evolution in decapods, and may have influenced their diversification into different osmotic niches. In semi-terrestrial crabs, hyper-osmoregulatory ability favors sojourns into burrows and dilute media, and provides a safeguard against hemolymph dilution; hypo-osmoregulatory ability underlies emersion capability and a life more removed from water sources. However, most comparative studies have neglected the roles of the phylogenetic and environmental components of inter-specific physiological variation, hindering evaluation of phylogenetic patterns and the adaptive nature of osmoregulatory evolution. Semi-terrestrial fiddler crabs (Uca) inhabit fresh to hyper-saline waters, with species from the Americas occupying higher intertidal habitats than Indo-west Pacific species mainly found in the low intertidal zone. Here, we characterize numerous osmoregulatory traits in all ten fiddler crabs found along the Atlantic coast of Brazil, and we employ phylogenetic comparative methods using 24 species to test for: (i) similarities of osmoregulatory ability among closely related species; (ii) salinity as a driver of osmoregulatory evolution; (iii) correlation between salt uptake and secretion; and (iv) adaptive peaks in osmoregulatory ability in the high intertidal American lineages. Our findings reveal that osmoregulation in Uca exhibits strong phylogenetic patterns in salt uptake traits. Salinity does not correlate with hyper/hypo-regulatory abilities, but drives hemolymph osmolality at ambient salinities. Osmoregulatory traits have evolved towards three adaptive peaks, revealing a significant contribution of hyper/hypo-regulatory ability in the American clades. Thus, during the evolutionary history of fiddler crabs, salinity has driven some of the osmoregulatory transformations that underpin habitat diversification, although others are apparently constrained phylogenetically.

The analysis of ratios of body measurements is deeply ingrained in the taxonomic literature. Whether for plants or animals, certain ratios are commonly indicated in identification keys, diagnoses, and descriptions. They often provide the only means for separation of cryptic species that mostly lack distinguishing qualitative characters. Additionally, they provide an obvious way to study differences in body proportions, as ratios reflect geometric shape differences. However, when it comes to multivariate analysis of body measurements, for instance, with linear discriminant analysis (LDA) or principal component analysis (PCA), interpretation using body ratios is difficult. Both techniques are commonly applied for separating similar taxa or for exploring the structure of variation, respectively, and require standardized raw or log-transformed variables as input. Here, we develop statistical procedures for the analysis of body ratios in a consistent multivariate statistical framework. In particular, we present algorithms adapted to LDA and PCA that allow the interpretation of numerical results in terms of body proportions. We first introduce a method called the \"LDA ratio extractor,\" which reveals the best ratios for separation of two or more groups with the help of discriminant analysis. We also provide measures for deciding how much of the total differences between individuals or groups of individuals is due to size and how much is due to shape. The second method, a graphical tool called the \"PCA ratio spectrum,\" aims at the interpretation of principal components in terms of body ratios. Based on a similar idea, the \"allometry ratio spectrum\" is developed which can be used for studying the allometric behavior of ratios. Because size can be defined in different ways, we discuss several concepts of size. Central to this discussion is Jolicoeur's multivariate generalization of the allometry equation, a concept that was derived only with a heuristic argument. Here we present a statistical derivation of the allometric size vector using the method of least squares. The application of the above methods is extensively demonstrated using published data sets from parasitic wasps and rock crabs.

The Japanese freshwater crab Geothelphusa dehaani species complex is distributed widely across the Japanese Archipelago. Despite its suggested high genetic and morphological diversity, key aspects such as nuclear DNA (nuDNA) population structure and relationship between body color patterns and genetic populations remain unclear. To address these gaps, this study analyzed genome-wide single nucleotide polymorphisms (SNPs) in nuDNA and mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) markers in samples from Hokkaido to the Tokara Islands, Japan. ADMIXTURE analysis identified five distinct populations with significant geographic boundaries. These populations exhibited unique geographical patterns, spanning across islands and enclave distribution, indicating that G . dehaani populations have been shaped by complex factors, including sea level changes and volcanic activity. Regional body color variations partially aligned with SNP clades. Further, combining body color with collection locality data could help identify the specimen populations. Contrasting patterns between mtDNA and nuDNA suggest historical gene flow and introgression, emphasizing the need for caution when interpreting earlier phylogenetic studies based on combined mtDNA and nuDNA sequences. Our findings provide a foundational baseline for future research into the taxonomy, phylogeny, and population dynamics of the G . dehaani species complex, advancing our understanding of its evolutionary history.

Crabs feed on a wide range of items and display diverse feeding strategies. The primary objective of this study was to investigate 10 digestive enzyme genes in representative crabs to provide insights into the genetic basis of feeding habits among crab functional groups. Crabs were classified into three groups based on their feeding habits: herbivores (HV), omnivores (OV), and carnivores (CV). To test whether crabs’ feeding adaptations matched adaptive evolution of digestive enzyme genes, we examined the 10 digestive enzyme genes of 12 crab species based on hepatopancreas transcriptome data. Each of the digestive enzyme genes was compared to orthologous sequences using both nucleotide- (i.e., PAML and Datamonkey) and protein-level (i.e., TreeSAAP) approaches. Positive selection genes were detected in HV crabs (AMYA, APN, and MGAM) and CV crabs (APN, CPB, PNLIP, RISC, TRY, and XPD). Additionally, a series of positive selection sites were localized in important functional regions of these digestive enzyme genes. This is the first study to characterize the molecular basis of crabs’ digestive enzyme genes based on functional feeding group. Our data suggest that HV crabs have evolved an enhanced digestion capacity for carbohydrates, and CV crabs have acquired digestion capacity for proteins and lipids.

Background China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. Results Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense , and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo- nad1 ) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo- trnL2 and pseudo- rrnL ) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. Conclusions This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures.