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.

Multi-gene phylogeny of the primary freshwater crab genus Ptychophallus Smalley, 1964 (Pseudothelphusidae: Ptychophallinae) from the Neotropical region

The diversity of primary freshwater crabs of Central America is underestimated and poorly known, specially when considering both Atlantic and Pacific drainages distribution. Among the family Pseudothelphusidae Ortmann, 1893, the genus Ptychophallus Smalley, 1964 was recently revised using morphological data and encompassing 14 valid species, which are distributed exclusively in Costa Rica and Panama. Despite the informative scenario constructed with this previous study, some uncertainties remained such as those related to the populations distributed along different drainages and the lack of complete information regarding the phylogenetic relationships among the species that belong to this genus. Our phylogenetic reconstruction based on multigenes revealed four lineages. Ptychophallus costaricensis, P. colombianus, P. lavallensis, P. montanus, and P. tumimanus are well-established species, while P. paraxanthusi, P. exilipes and P. tristani were recovered as non-monophyletic in some relationships. Ptychophallus tristani and P. paraxanthusi were determined to be close relatives one with other, but with some representatives showing no clear correspondence and positioning in the molecular phylogeny, which raised doubts about the validity as separate species and/or the accuracy of identifications for some GenBank sequences. Ptychophallus tumimanus and P. montanus are morphologically very similar, but they are positioned in distinct clades. The genetic results confirmed a previous proposal that P. barbillaensis is a junior synonym of P. uncinatus, and P. bilobatus is closely related to P. uncinatus. The findings revealed the presence of one peculiar lineage with one species from Costa Rica compound by the resurrected P. campylus and another species from Costa Rica, originally identified as "P. cf. exilipes"; its morphology, however, did not match with any other analyzed species, which requires further analysis. Finally, possible misidentification in some sequences deposited in the GenBank were detected and should be reviewed. The reconstructed molecular phylogeny for the genus that inhabits both Atlantic and Pacific drainages of Central America provides a better understanding of the knowledge on the evolution of freshwater crabs and represents key information that will serve as baseline for further taxonomic studies on the cryptic biodiversity of this group.

Phylogeography of the true freshwater crab, Geothelphusa dehaani: Detected dual dispersal routes via land and sea

Dispersal is an important factor that determines the potential for colonization to pioneer sites. Although most decapods employ seaward migration for reproduction with a planktonic larval phase, true freshwater crabs spend their entire life cycle in freshwater. Therefore, it is expected that genetic regionality can be easily detected. In this study, we focused on true freshwater crabs, Geothelphusa Stimpson, 1858. Herein, we reveal the evolutionary history and dispersal patterns of freshwater crustaceans. We collected and genetically analyzed 283 specimens at 138 localities across the Japanese Islands. Phylogenetic analyses were conducted on the combined dataset (mtDNA COI, 16S, and nDNA ITS1, histone H3 regions) and the data set based on the mtDNA COI region. The phylogenetic relationships detected 10 clades that were highly monophyletic. The highlights of this study were the discovery of several cryptic species or undescribed species, and the completely different heterogeneous dual dispersal pathways within a single species; i.e., both land and ocean routes. Although it was concluded that Japanese crabs are basically genetically divided by straits, strong evidence for dispersion via ocean currents was also detected (i.e., a "sweepstake"). It was also confirmed that Geothelphusa dehaani (White, 1847) could survive in seawater.

A new species of freshwater crab of the genus Chaceus Pretzmann, 1965 (Brachyura: Decapoda: Pseudothelphusidae) from La Guajira, including distribution and a key to the species of the genus

We describe and illustrate a new species of Chaceus Pretzmann, 1965, from the Regional Natural Park of the Serranía de Perijá, La Guajira Department, Colombia. This increases the number of Chaceus species to ten, three of them with records only from Venezuela. The species of this genus are distributed in the Sierra de Santa Marta of Colombia and the Serranía de Perijá of Colombia and Venezuela. We distinguished the new species from its congeners mainly by the third maxilliped, with an exopod that is 0.60-0.62 the length of ischium, and by the morphology of the first male gonopod, particularly by the shapes of the mesial, marginal, and lateral processes. We include the distribution of the Chaceus species here and a key for the identification of the species based on the morphology of the first male gonopod.

The evolutionary journey of freshwater crabs of the genus Potamon (Decapoda: Brachyura: Potamidae)

AIM

Freshwater ecosystems host a rich biodiversity, including freshwater crabs. The family Potamidae is a diverse group of freshwater crabs with a Palearctic and Oriental distribution. Specifically, the genus Potamon is found in the Middle East, Southern Europe, and Northern Africa. Potamon species are considered true freshwater crabs due to their total independence from the marine environment, which makes them idea organisms to study historical freshwater connectivity dynamics. In this study we aim to elucidate the phylogenetic relationships of the genus Potamon and discuss the historical freshwater connectivity in the Mediterranean region.

METHODS

Here we use up to eleven genetic markers to reconstruct a robust phylogenetic tree of the group and use Bayesian methods to time-calibrate the tree. We further use historical biogeography methods implemented in a Bayesian framework to assess the ancestral distribution ranges of the group.

RESULTS

In this study we generate the most complete dataset for the group, covering practically the whole distribution range of the genus. We obtained a robust phylogenetic hypothesis and evaluated the times of divergence of the group. The result of the historical biogeography shows the evolution of historical distribution ranges of species of Potamon.

MAIN CONCLUSIONS

The Mediterranean Sea is placed in a key intersection for the exchange of fauna and flora. Here we present evidence for the potential of freshwater fauna exchange, through the Mediterranean Sea after a period of desiccation and the loss of contact with the ocean. The origin of Potamon genus is found to be in Western Asia, probably Eastern Iran.

Two new genera and one new species of freshwater crabs of the subfamily Pseudothelphusinae (Decapoda: Brachyura: Pseudothelphusidae) from southwestern Mexico

Two new genera from the Chimalapas region in eastern Oaxaca, and from Zongolica, Veracruz, Mexico are presented. Mokayathelphusa angelsotoi n. gen., n. sp., which is described from Oaxaca, is placed in the subfamily Pseudothelphusinae due to the presence of a caudomarginal projection that ends apically in an ornamented plate. Alvarezius n. gen. is erected to accommodate A. zongolicae (Alvarez, Villalobos & Moreno, 2012) n. comb. This species was described in Pseudothelphusa, but a recent molecular phylogenetic analysis based on partial sequences of three genes (COI, 16S and H3) places this species outside the genus Pseudothelphusa and as a sister lineage to Tehuana. These results in combination with a morphological analysis support the establishment of the new genus.  

Revision of the freshwater crabs of the genus Tehuana Rodríguez & Smalley in Smalley 1970 (Decapoda, Pseudothelphusidae), with the descriptions of two new species

The freshwater crab genus Tehuana Rodríguez & Smalley in Smalley, 1970 includes eight species distributed in southeastern Mexico. A recent review of organisms belonging to this genus uncovered new variations in the male gonopod morphology. A phylogenetic analysis based on molecular characters using three genes (H3, 16S, and COI) resulted in the identification of two new species which are described herein: Tehuanaayotzintepecensis sp. nov. from Oaxaca and Tehuanacol sp. nov. from Veracruz. New diagnoses are provided for those species that had very brief descriptions lacking the treatment of important taxonomic characters and an identification key for all the species in the genus is also given. A discussion of the distribution of all the species in Tehuana in the Isthmus of Tehuantepec is presented.

Barcoding and species delimitation of Iranian freshwater crabs of the Potamidae family (Decapoda: Brachyura)

Freshwater ecosystems are under multiple threats in modern times such as water extraction for human consumption, industries and agricultural activities, water contamination and habitat destruction for example. At the same time the biodiversity of these ecosystems are often poorly studied, especially in arid countries such as Iran. In this work, we study one of the ecologically important members of Iranian freshwater fauna, freshwater crab species of the genus Potamon. Here, we barcoded the different populations occurring in the country and delimited the species to allow for a better understanding of their distribution and taxonomy. In this study, we evaluated the taxonomical statues of Potamon species in Iran using genetic data. In addition, we created the first barcoding reference for Iranian freshwater crabs, which is an important resource for future environmental and conservation studies.

Multigene phylogeny and taxonomic revision of American shrimps of the genus Cryphiops Dana, 1852 (Decapoda, Palaemonidae) implies a proposal for reversal of precedence with Macrobrachium Spence Bate, 1868

The freshwater shrimp genus Cryphiops Dana, 1852 has a disjunct distribution in North (Mexico) and South (Brazil, Chile) America, and is composed of only six species. The current classification of genera in the Palaemonidae is controversial, based on variable morphological characters, and still far from a clear definition. Cryphiops differs from the speciose genus Macrobrachium Spence Bate, 1868 only by the absence of the hepatic spines on the carapace. Previous studies with a limited dataset suggested the necessity to link morphology and phylogeny to create an internal rearrangement in the genus to resolve the paraphyletic status. Through a molecular phylogenetic approach, the evolutionary relationships are inferred based on four (mitochondrial and nuclear) genes, among all recognized species of Cryphiops and, in combination with a taxonomic revision, a rearrangement in the systematics of the genus is suggested. The absence of hepatic spines on the carapace, the only character used to separate the genus Cryphiops, is subjective and should be considered as a homoplasy. This implies that Cryphiops and Macrobrachium are subjective synonyms and, because the latter genus is much more diverse and widely known, with several economically important species, to avoid confusion and disturbance in nomenclatural stability and keep universality, a proposal for the priority of the older synonym (Cryphiops) to be partially suppressed in favor of maintaining the prevailing use of the younger synonym (Macrobrachium) is presented. As the species of Cryphiops should be accommodated in the genus Macrobrachium, new names to replace three preoccupied specific names that, by this action, resulted to be secondary homonyms are offered.