Out of the Sichuan Basin: Rapid species diversification of the freshwater crabs in Sinopotamon (Decapoda: Brachyura: Potamidae) endemic to China

Diversification of freshwater crabs on the sky islands in the Hengduan Mountains Region, China

The numerous naturally-fragmented sky islands (SIs) in the Hengduan Mountains Region (HMR) of southwestern China constitute discontinuous landscapes where montane habitats are isolated by dry-hot valleys which have fostered exceptional species diversification and endemicity. However, studies documenting the crucial role of SI on the speciation dynamics of native freshwater organisms are scarce. Here we used a novel set of comprehensive genetic markers (24 nuclear DNA sequences and complete mitogenomes), morphological characters, and biogeographical information to reveal the evolutionary history and speciation mechanisms of a group of small-bodied montane potamids in the genus Tenuipotamon. Our results provide a robustly supported phylogeny, and suggest that the vicariance events of these montane crabs correlate well with the emergence of SIs due to the uplift of the HMR during the Late Oligocene. Furthermore, ancestrally, mountain ridges provided corridors for the dispersal of these montane crabs that led to the colonization of moist montane-specific habitats, aided by past climatic conditions that were the crucial determinants of their evolutionary history. The present results illustrated that the mechanisms isolating SIs are reinforced by the harsh-dry isolating climatic features of dry-hot valleys separating SIs and continue to affect local diversification. This offers insights into the causes of the high biodiversity and endemism shown by the freshwater crabs of the HMR-SIs in southwestern China.

The systematic position of Cryptopotamonanacoluthon (Kemp, 1918), with the description of a new species of Sinolapotamon Tai & Sung, 1975 (Crustacea, Decapoda, Brachyura, Potamidae) from southern China

The systematics of the potamid freshwater crab Cryptopotamonanacoluthon (Kemp, 1918) is clarified, and its generic position in Sinolapotamon Tai & Sung, 1975, is confirmed based on morphological comparisons, geographical information and phylogenetic analyses. A new species of Sinolapotamon, Sinolapotamoncirratumsp. nov. is described from the Guangxi Zhuang Autonomous Region of China. Sinolapotamoncirratumsp. nov. is distinguished from its congeners by the combination of characters of its carapace, third maxilliped, anterolateral margin, and unique male first gonopod. Phylogenetic analyses based on partial COX1, 16S rRNA and 28S rRNA genes also support the species as new.

Adaptive evolution characteristics of mitochondrial genomes in genus Aparapotamon (Brachyura, Potamidae) of freshwater crabs

BACKGROUND

Aparapotamon, a freshwater crab genus endemic to China, includes 13 species. The distribution of Aparapotamon spans the first and second tiers of China's terrain ladder, showing great altitudinal differences. To study the molecular mechanisms of adaptive evolution in Aparapotamon, we performed evolutionary analyses, including morphological, geographical, and phylogenetic analyses and divergence time estimation. We sequenced the mitogenomes of Aparapotamon binchuanense and Aparapotamon huizeense for the first time and resequenced three other mitogenomes of Aparapotamon grahami and Aparapotamon gracilipedum. These sequences were combined with NCBI sequences to perform comparative mitogenome analysis of all 13 Aparapotamon species, revealing mitogenome arrangement and the characteristics of protein-coding and tRNA genes.

RESULTS

A new species classification scheme of the genus Aparapotamon has been detected and verified by different aspects, including geographical, morphological, phylogenetics and comparative mitogenome analyses. Imprints from adaptive evolution were discovered in the mitochondrial genomes of group A, including the same codon loss at position 416 of the ND6 gene and the unique arrangement pattern of the tRNA-Ile gene. Multiple tRNA genes conserved or involved in adaptive evolution were detected. Two genes associated with altitudinal adaptation, ATP8 and ND6, which experienced positive selection, were identified for the first time in freshwater crabs.

CONCLUSIONS

Geological movements of the Qinghai-Tibet Plateau and Hengduan Mountains likely strongly impacted the speciation and differentiation of the four Aparapotamon groups. After some group A species dispersed from the Hengduan Mountain Range, new evolutionary characteristics emerged in their mitochondrial genomes, facilitating adaptation to the low-altitude environment of China's second terrain tier. Ultimately, group A species spread to high latitudes along the upper reaches of the Yangtze River, showing faster evolutionary rates, higher species diversity and the widest distribution.

Insights into the Gut Microbiota of the Freshwater Crab Sinopotamon planum across Three Seasons and Its Associations with the Surrounding Aquatic Microbiota

Gut microbiota is closely related to the health of the host and its adaptation to environmental changes. Sinopotamon planum is a species of freshwater crab that lives in the water for three seasons and plays a key role in freshwater ecosystems as a benthic macroinvertebrate, an important indicator of aquatic ecological health. In this study, we sequenced 60 gut microbial samples of S. planum and nine microbial samples from the surrounding water in spring, summer, and autumn based on the 16S rRNA gene. The results showed that gut microbiota had the highest alpha diversity in summer, which may be related to increased adaptability in summer. Firmicutes, Proteobacteria, and Bacteroidota were the most dominant phyla of gut microbiota across three seasons, with Candidatus Hepatoplasma and Candidatus Bacilloplasma being the main genera. These main phyla and genera may be key to maintaining a stable function of the intestinal environment. Firmicutes was the phylum with the highest relative abundance, which is probably related to the carnivorous behaviour of S. planum. The abundant C. Hepatoplasma may be related to the starvation of S. planum in the wild. In both gut and water microbiota, beta diversity analyses showed significant differences across seasons. Comparative analysis of gut microbes and surrounding water microbes showed significant differences in microbial diversity and composition between gut and surrounding water. In conclusion, the structure of the gut microbial community of S. planum differed significantly between the studied seasons, but the water microbial community around S. planum was less variable and significantly different from the gut microbes. The seasonal differences in gut microbes are more likely the result of self-internal adaptation to changes in water temperature and food resources between seasons.

Mitochondrial genomic characterization of two endemic Chinese freshwater crabs of the genus Sinopotamon (Brachyura: Potamidae) and implications for biogeography analysis of Potamidae

As an endemic freshwater crab group in China, the phylogenetic relationships within Sinopotamon are still controversial because of the limited taxon samples. In this study, the complete mitogenomes of Sinopotamon chishuiense with 17,311 bp and the nearly complete mitogenomes of S. wushanense with 16,785 bp were firstly sequenced and analyzed. Compared with other reported mitogenomes of Potamidae, some novel patterns of gene rearrangement were detected in these two Sinopotamon mitogenomes, which could be illuminated by the mechanisms of tandem duplication-random loss, recombination, and translocation. Phylogenetic analyses showed the nonmonophyly of the Sinopotamon and a sister group relationship with Tenuilapotamon. These crabs from the eastern and southern of the Yangtze River basin were more closely related while other crabs form the plateau areas formed a separate clade. Divergence time indicated that the Sinopotamon and its sister group Tenuilapotamon diverged from other potamiscine freshwater crabs approximately 42.65 Mya, which belongs to the recent main uplifts period of the Tibetan Plateau in the Late Miocene. Combined with the similar evolutionary rates and relatively stable habitat altitude of these Sinopotamon species, these results implied that the ecological environment may be relatively stable during the speciation. Overall, our study yielded worthy perceptions for the evolutionary and taxonomic relationship of Sinopotamon and will help to better clarify the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Sinopotamon. Overall, our study yielded valuable insights into the evolutionary history and taxonomic relationship of Sinopotamon and these results will help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Sinopotamon.

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 species of freshwater crab of the genus Aparapotamon Dai & Chen, 1985 (Crustacea, Brachyura, Potamidae) from Yunnan, China

Two new species of freshwater crab of the genus Potamid Aparapotamon Dai & Chen, 1985 are described from Yunnan Province, southwest China. Morphological comparisons were made between the two new species and type materials of other 11 species of Aparapotamon. Aparapotamonbinchuanensesp. nov. and A.huizeensesp. nov. can be separated from their congeners by the shape of the epibranchial tooth, the frontal view of the cephalothorax, the male first gonopod, and the female vulvae. The molecular analyses based on partial mitochondrial 16S rRNA gene are also included. This study brings the number of Aparapotamon species to 13.

Description of two new species of the genus Heterochelamon Türkay & Dai, 1997 (Crustacea: Decapoda: Brachyura: Potamidae), from southern China

This study describes two new species of freshwater crab of the genus Heterochelamon Türkay & Dai, 1997 from southern China, H. huidongense from Guangdong Province and H. jinxiuense from Guangxi Zhuang Autonomous Region. The two new species can be differentiated from congeners by characters derived from the shape of the epibranchial tooth, external orbital angle, cheliped proportions and structure of the male first gonopod. The present study brings the number of Heterochelamon species to seven. We used the mitochondrial 16S rRNA gene for a molecular analysis and the results are consistent with the morphological features that support the recognition of two new taxa.

Clone, identification and functional characterization of a novel toll (Shtoll1) from the freshwater crab Sinopotamon henanense in response to cadmium exposure and Aeromonas hydrophila infection

Toll is essential in innate immune system which is important for defense against bacterial, fungal and viral infections in invertebrates. Our previous study showed that cadmium (Cd) could change the expression pattern of ShToll3 in the epithelium (gills and midgut from the freshwater crab Sinopotamon henanense) infected by Aeromonas hydrophila. To investigate the diverse innate immune roles of crustacean homolog Tolls, in this study, we cloned Shtoll1 from S. henanense. The full-length cDNA of Shtoll1 was 4746 bp, with an ORF of 3033 bp encoding a putative protein of 111 amino acids, a 5'-untranslated region of 255 bp and a 3'-untranslated region of 1713 bp. Phylogenetic analysis showed that ShToll1 was clustered into the group of DmToll1, DmToll 4 and DmToll 5. In addition, the tissue distribution results showed that Shtoll1 was expressed widely in different tissues, with the highest expression in heamocytes. Besides, Shtoll1 expressions were upregulated in heamocytes and hepatopancreas after A. hydrophila infection. At the same time, the increase of Shtoll1 expressions were examined in heamocytes in response to Cd exposure and A. hydrophila infection in combination. Through western blotting and immunohistochemical analysis, the ShToll1 expressions in heamocytes were increased in response to A. hydrophila and Cd independently as well as in combination. Moreover, the mRNA level of three antimicrobial peptides (AMPs) alf5, alf6, and c-lys, which possibly responded to Cd and A. hydrophila stimulation through Shtoll1, were analyzed. Thus, we conclude that Cd expand the susceptibility of ShToll1 to A. hydrophila infection in heamocytes. This suggest that ShToll1 may contribute to the innate immune defense of S. henanense against A. hydrophila and Cd in heamocytes.

Rapid divergent coevolution of Sinopotamon freshwater crab genitalia facilitates a burst of species diversification

One of the most striking radiations in brachyuran evolution is the considerable morphological diversification of the external reproductive structures of primary freshwater crabs: the male first gonopod (G1) and the female vulva (FV). However, the lack of quantitative studies, especially the lack of data on female genitalia, has seriously limited our understanding of genital evolution in these lineages. Here we examined 69 species of the large Chinese potamid freshwater crab genus Sinopotamon Bott, 1967 (more than 80% of the described species). We used a landmark-based geometric morphometric approach to analyze variation in the shape of the G1 and FV, and to compare the relative degree of variability of the genitalia with non-reproductive structures (the third maxillipeds). We found rapid divergent evolution of the genitalia among species of Sinopotamon when compared to non-reproductive traits. In addition, the reconstruction of ancestral groundplans, together with plotting analyses, indicated that the FV show the most rapid divergence, and that changes in FV traits correlate with changes in G1 traits. Here we provide new evidence for coevolution between the male and female external genitalia of Sinopotamon that has likely contributed to rapid divergent evolution and an associated burst of speciation in this lineage.

A new species of karst-dwelling freshwater crab of the genus Chinapotamon Dai & Naiyanetr, 1994 (Crustacea: Decapoda: Brachyura: Potamidae), from Guizhou, southwest China

Chinapotamon maolanense sp. n. from Maolan National Nature Reserve, Guizhou, southwest China, is described. C. maolanense sp. n. has diagnostic features of Chinapotamon, such as a slender and sinuous male first gonopod, prominently convex carapace, and one-third ratio of frons to carapace width. This new species can be distinguished from congeners by the combination of the following characters: relatively slender subterminal segment of the first gonopods, nearly oval-shaped carapace, anterolateral margin cristate of carapace and an oval-shaped gap between the fingers of the male major chela. In addition, we used a 16S rRNA gene fragment to explore the relationship between C. maolanense sp. n. and C. glabrum, C. depressum and other freshwater crabs distributed in Guizhou; the results support the new species being assigned to Chinapotamon and clearly different from other species used in the analysis.

Identification of a novel toll gene (Shtoll3) from the freshwater crab Sinopotamon henanense and its expression pattern changes in response to cadmium followed by Aeromonas hydrophila infection

Toll signaling is essential for expression of immune genes which are important for defense against bacterial, fungal and viral infections in invertebrates. Although several toll genes have been identified in the crustaceans, none of them has been investigated in freshwater crab Sinopotamon henanense. Moreover, the effect of cadmium (Cd) on toll gene expression has never been examined on the freshwater crabs which live in the sediments and are prone to heavy metal bioaccumulation. Our transcriptomic analysis of hepatopancreas tissue reveals that toll3 gene expression has been decreased when treated with Cd. In this study, we cloned one toll gene (hereby designated Shtoll3) from the crab. The full-length cDNA of Shtoll3 was 4488 bp, with an ORF of 3693 bp encoding a putative protein of 1230 amino acids, a 5'-untranslated region of 414 bp and a 3'-untranslated region of 781 bp. Phylogenetic analysis showed that ShToll3 was clustered into the group of DmToll8. The tissue distribution results showed that Shtoll3 was expressed widely in different tissues, with the highest in gills, and the lowest in hemocytes. Shtoll3 expression was down-regulated only in midguts after Aeromonas hydrophila infection. With Cd presence, Shtoll3 expression in response to A. hydrophila were up-regulated in midguts and gills, which was further confirmed by western blotting analysis. Moreover, the mRNA level of two antimicrobial peptides (AMPs) crustin and c-lys, which possibly responded to Cd and A. hydrophila stimulation through Shtoll3, were analysised. Thus, we conclude that Cd changes the susceptibility of Shtoll3 to A. hydrophila infection in gills and midguts. This suggest that Shtoll3 may contribute to the innate immune defense of S. henanense to A. hydrophila and Cd can modify the immune function in epithelium.

Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae)

Recent morphological and molecular evidence has challenged classical interpretations of eubrachyuran phylogeny and evolution. Complete mitochondrial genomes of two species of potamid freshwater crabs, Sinopotamon yaanense and Sinopotamon yangtsekiense were obtained using next-generation sequencing. The results revealed a novel gene order with translocations of a five-gene block and a tRNA gene in comparison to available brachyuran mitochondrial genomes. DNA sequence comparisons position the Potamidae, a primary freshwater crab family, outside of the clade for the traditional heterotreme families, and closer to the clade that includes the thoracotreme families of grapsoid and ocypodoid crabs. Mitogenomic comparisons using rapid next-generation sequencing and a much wider taxonomic sample are required for a high-resolution examination of the phylogenetic relationships within the Eubrachyura.