Drawn to the dark side: a molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses.

Atyid freshwater shrimps are globally distributed and form an important part of freshwater ecosystems, particularly in the tropics and subtropics. Despite their widespread distribution and ecological importance, their phylogenetic relationships are largely unresolved. Here we present the first comprehensive molecular phylogeny of the Atyidae investigating the evolutionary relationships among 32 of the 42 genera using mitochondrial and nuclear markers. Our data indicate that the established classification of the Atyidae is in need of substantial taxonomic revision at all taxonomic levels. We suggest a new suprageneric systematization of atyids and discuss problematic issues at the generic level, particularly in the most speciose genus, Caridina. Molecular clock based divergence time estimates for atyids vary widely, but invariably support the assumption that atyids are an ancient freshwater lineage with an origin in the mid-Cretaceous at the very latest. Atyid distribution patterns are the result of instances of both long-distance dispersal and vicariance, depending largely on the reproductive mode of taxa. From an evolutionary perspective, the high frequency of independent origin of both a complete (landlocked) freshwater life cycle and a cave-dwelling mode of life is remarkable and unparalleled among crustaceans.

Evolution of life history traits in Asian freshwater prawns of the genus Macrobrachium (Crustacea: Decapoda: Palaemonidae) based on multilocus molecular phylogenetic analysis.

Freshwater prawns of the genus Macrobrachium are free-living decapod crustaceans that are commonly encountered in tropical streams and lakes. We present a molecular phylogenetic analysis of the diverse Southeast and East Asian fauna based on >3 kb sequence data from three nuclear and two mitochondrial markers for almost 50% of the described fauna. We reconstruct the phylogenetic relationships and track the evolution of key life history traits. Our tree suggests that the last common ancestor of the Asian Macrobrachium laid numerous small eggs and had prolonged larval development ("PLD") in saline coastal waters after which the adults matured in freshwater habitats. We also argue for five independent losses of the marine larval phase to yield five clades of species that develop entirely in freshwater and have fewer and larger eggs than the species with PLD. These species have either semi-abbreviated (two origins) with at least one free-swimming stage or abbreviated larval development ("ALD": three origins) which lack free-swimming larvae. A Shimodaira-Hasegawa test rejects all trees that would imply a single loss of the marine larval phase, but alternative and equally parsimonious optimizations exist that imply a smaller number of losses. However, these scenarios would require the re-acquisition of free-swimming larvae. A concentrated-change test supports Pereira and Garcia's [Pereira, G.A., Garcia, J.V., 1995. Larval development of Macrobrachium reyesi Pereira (Decapoda, Palaemonidae), with a discussion on the origin of abbreviated development in palaemonids. J. Crust. Biol. 15, 117-133] hypothesis of a significant correlation between living in freshwater and the origin of semi-abbreviated and abbreviated larval development. Our phylogenetic tree also reveals that Asian Macrobrachium have independently become cavernicolous at least twice, and invaded the highly acidic waters of freshwater and peat swamps two or three times.

Neocaridinafonticulata, a new land-locked freshwater shrimp from Hengchun Peninsula, Taiwan (Decapoda, Caridea, Atyidae).

A new species of land-locked freshwater shrimp, Neocaridinafonticulata sp. n. (Atyidae), is described from Kenting, Hengchun Peninsula, Pingtung County, southern Taiwan. This new species can be distinguished from its congeners by rostrum structure, pereiopods, and male first and second pleopods. The molecular evidence of mitochondrial cytochrome oxidase subunit I (COI) also supports the establishment of a new species. This is the third endemic species of Neocaridina known from Taiwan.

Freshwater Shrimps from Karst Caves of Southern China, with Descriptions of Seven New Species and the Identity of Typhlocaridina linyunensis Li and Luo, 2001 (Crustacea: Decapoda: Caridea).

Yixiong Cai and Peter Kee Lin Ng (2018) Seven new atyid shrimp species of the genus Caridina H. Milne Edwards, 1837 are described from southern China: C. longshan sp. nov., C. alu sp. nov., C. spinicrus sp. nov., C. beiliu sp. nov., C. jiangkou sp. nov., C. guilin sp. nov. and C. laticarpalis sp. nov. Descriptions and figures for all taxa are provided, and taxa are compared with their closest congeners. An updated list of all cave atyid and palaemonid shrimp species found in China is provided. Caridina semiblepsia Guo, Choy and Gui, 1996 is here regarded as a junior subjective synonym of C. ablepsia Guo, Jiang and Zhang, 1992. One poorly known species, Typhlocaridina linyunensis Li and Luo, 2001, described from a cave in Guangxi is here shown to be a palaemonid instead of an atyid, and is actually the senior synonym of Macrobrachium lingyunense Li, Cai and Clarke, 2006.

The complete mitochondrial genome of Somanniathelphusa boyangensis and phylogenetic analysis of Genus Somanniathelphusa (Crustacea: Decapoda: Parathelphusidae).

In this study, the authors first obtained the mitochondrial genome of Somanniathelphusa boyangensis. The results showed that the mitochondrial genome is 17,032bp in length, included 13 protein-coding genes, 2 rRNAs genes, 22 tRNAs genes and 1 putative control region, and it has the characteristics of the metazoan mitochondrial genome A+T bias. All tRNA genes display the typical clover-leaf secondary structure except tRNASer(AGN), which has lost the dihydroxyuridine arm. The GenBank database contains the mitochondrial genomes of representatives of approximately 22 families of Brachyura, comprising 56 species, including 4 species of freshwater crab. The authors established the phylogenetic relationships using the maximum likelihood and Bayesian inference methods. The phylogenetic relationship indicated that the molecular taxonomy of S. boyangensis is consistent with current morphological classification, and Parathelphusidae and Potamidae are derived within the freshwater clade or as part of it. In addition, the authors used the COX1 sequence of Somanniathelphusa in GenBank and the COX1 sequence of S. boyangensis to estimated the divergence time of this genus. The result displayed that the divergence time of Somanniathelphusa qiongshanensis is consistent with the separation of Hainan Island from mainland China in the Beibu Gulf, and the divergence time for Somanniathelphusa taiwanensis and Somanniathelphusa amoyensis is consistent with the separation of Taiwan Province from Mainland China at Fujian Province. These data indicate that geologic events influenced speciation of the genus Somanniathelphusa.

The complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) with phylogenetic implications for freshwater crabs.

In the present study, we determined the complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) for the first time. The genome is 15,380bp in length and typically consists of 37 genes. When the gene order was compared to the ancestral crustacean type, two tRNA genes (tRNAHis and tRNAGln) were rearranged in H. lichuanense, and the translocation of tRNAGln appeared only in Potamoidea crabs, such as Geothelphusa dehaani and Sinopotamon xiushuiense, supporting the monophyly of the Potamoidea superfamily. Thirteen protein-coding genes and 2 rRNA genes were divided into five complexes to perform the phylogenetic analysis, and the results showed that the trees constructed by complex I (ND1-ND6 and ND4L), complex IV (COX1-COX3) and rRNA genes better accord with the morphological classification system, suggesting that molecular markers of higher-level phylogeny can be developed in these three complexes in the future. The estimated divergence time for freshwater crabs is approximately 133.58Ma, and G. dehaani from Japan diverged from the freshwater crabs of mainland China approximately 60.66Ma. A selective pressure analysis based on current data revealed obviously increasing dN/dS ratios (except for ATP6 and ND4L) of freshwater crabs, and the accumulation of nonsynonymous mutations suggests that terrestrial habitats provide a relatively relaxed selective pressure environment for this group.

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes.

Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km2 of five low order hill streams within the highly urbanized island city-state of Singapore. We compared populations of J. singaporensis with that of the non-threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata, and found surprisingly high congruence between their population genomic histories. Based on 2,617 and 2,470 genome-wide SNPs mined via the double-digest restriction-associated DNA sequencing method for ~90 individuals of J. singaporensis and P. maculata, respectively, the populations are strongly isolated (FST = 0.146-0.371), have low genetic diversity for both species (also for COI), and show signatures of recent genetic bottlenecks. The most genetically isolated populations for both species are separated from other populations by one of the oldest roads in Singapore. These results suggest that anthropogenic developments may have impacted stream-dependent species in a uniform manner, regardless of ubiquity, habitat preference, or dispersal modes of the species. While signs of inbreeding were not detected for the critically endangered species, the genetic distinctiveness and low diversity of the populations call for genetic rescue and connecting corridors between the remaining fragments of the natural habitat.

A New Species of Land-locked Freshwater Shrimp of the Genus Neocaridina (Decapoda: Caridea: Atyidae) from Iki Island, Kyushu, Japan.

Hsi-Te Shih, Yixiong Cai, Nobuaki Niwa, and Yasuhiko Nakahara (2017) A new species of land-locked freshwater shrimp, Neocaridina ikiensis (Decapoda: Caridea: Atyidae), is described from Iki Island, Kyushu, Japan, based on morphological and molecular evidence. This new species can be distinguished from its congeners by a suite of characters, including rostrum structure, number of post-orbital rostral teeth, male first and second pleopods and telson structure. The molecular evidence of mitochondrial cytochrome oxidase subunit I (COI) shows this species has sufficient interspecific divergence, and its high intraspecific variation suggests that it evolved on this island over a long period of time. Based on the molecular clock estimation, the speciation of N. ikiensis n. sp. is supposed to be related with the quiescent periods of volcanoes on this island. This is the second native species of Neocaridina known, after N. denticulata (De Haan, 1844), from the main islands of Japan.

Dead shrimp blues: a global assessment of extinction risk in freshwater shrimps (Crustacea: Decapoda: Caridea).

We present the first global assessment of extinction risk for a major group of freshwater invertebrates, caridean shrimps. The risk of extinction for all 763 species was assessed using the IUCN Red List criteria that include geographic ranges, habitats, ecology and past and present threats. The Indo-Malayan region holds over half of global species diversity, with a peak in Indo-China and southern China. Shrimps primarily inhabit flowing water; however, a significant subterranean component is present, which is more threatened than the surface fauna. Two species are extinct with a further 10 possibly extinct, and almost one third of species are either threatened or Near Threatened (NT). Threats to freshwater shrimps include agricultural and urban pollution impact over two-thirds of threatened and NT species. Invasive species and climate change have the greatest overall impact of all threats (based on combined timing, scope and severity of threats).

Freshwater shrimp-sponge association from an ancient lake.

Shrimp-sponge associations occur frequently in marine ecosystems, serving as model systems for the evolution of eusociality. Here, we describe the first known instance of such association in freshwater from an ancient lake in Indonesia. The shrimp Caridina spongicola forms an exclusive and probably commensal association with a yet undescribed spongillinid sponge. Phylogenetic and ecological data suggest a comparatively recent origin of both taxa. Climatic fluctuations may have facilitated speciation and occasional hybridization of the shrimp species, which is derived from a rock-dwelling ancestor. Their extremely localized occurrence in an increasingly disturbed area makes both taxa a conservation priority.