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.     

Phylogeographic patterning in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes) reveals the signature of historical climatic oscillations

Aim The phylogeographic relationships among populations of the common Cape River crab, Potamonautes perlatus, are examined to investigate whether the contemporary population genetic structure is congruent with the hypothesized hydrographic evolution of drainage systems established during the Pliocene, or whether it reflects an older Miocene climatic amelioration. Location 139 samples of P. perlatus were collected from 31 populations distributed among the five major perennial drainage systems and a number of smaller catchments in the Western and Eastern Cape, South Africa. Methods Phylogeographic analysis using parsimony, maximum likelihood, minimum evolution and Bayesian inferences was employed for the 16S rRNA mtDNA gene region, while bootstrapping and posterior probabilities were used to assess the robustness of clades. In addition, nested clade analysis was performed in an attempt to disentangle the contemporary and historical factors that have sculpted genealogical relationships among conspecific populations of P. perlatus. Results Phylogenetic topologies were congruent irrespective of the evolutionary method employed. Two highly distinct reciprocally monophyletic clades characterized by marked levels of corrected sequence divergence were present, with no shared haplotypes between the two major phylogroups. Phylogroup one comprises the populations of the westward‐flowing drainages (mainly the Berg and Olifants drainages), and phylogroup two comprises all of the southward‐flowing drainages and can further be divided into two subclades – one containing the Breede River populations, and the other containing the Gamtoos and Gourits drainage systems. The nested clade analysis demonstrated restricted gene flow and long‐distance dispersal for a number of higher clade levels. The higher‐level groups and results for the total cladogram suggest either fragmentation or isolation by distance. Main conclusions Freshwater crabs are generally highly philopatric, and dispersal, although not common, has occurred historically. The westward‐flowing drainages (Berg, Olifants, Eerste, Liesbeeck and Tokai) are isolated from the southward‐flowing drainages by the Cape Fold Mountains, while the southward‐flowing drainages have a number of tributaries that extend into the low‐lying regions, allowing for gene flow between these three major drainages systems (Breede, Gamtoos and Gourits). Among the westward‐flowing drainages, a more intensive sampling regime is required to understand evolutionary relationships. Our molecular results suggest that the observed patterns pre‐date the formation of contemporary hydrographic patterns in the Cape. This suggests that an older Late Miocene event has severely impacted the contemporary population structure in this species, as recent Pliocene hydrographic boundaries do not correspond to the phylogeographic pattern observed. Conservation efforts for aquatic taxa should clearly be directed at the catchments, in an attempt to conserve biological diversity.     

Global diversity of crabs (Crustacea: Decapoda: Brachyura) in freshwater

An assessment of the global freshwater crab diversity is presented. A total of 1,476 species in 14 families are currently known from all zoogeographical regions (except Antarctica), including 1,306 species in eight exclusively freshwater families (Pseudothelphusidae, Trichodactylidae, Potamonautidae, Deckeniidae, Platythelphusidae, Potamidae, Gecarcinucidae and Parathelphusidae). Estimates of true freshwater crab diversity including likely numbers of undescribed taxa suggest that the field remains largely in a “discovery” phase. Main ideas on the origins, diversification, and phylogeny of true freshwater crabs are briefly discussed. The economic importance of freshwater crabs is also highlighted. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Global diversity of crabs (Aeglidae: Anomura: Decapoda) in freshwater

The freshwater anomuran crabs of the family Aeglidae are all restricted to southern South America occurring in Chile, Brazil, Bolivia, Uruguay, Paraguay, and Argentina. The family consists of a single genus, Aegla, containing 63 currently described species. There are another 5–10 known yet undescribed species to complement this diversity. The aeglids occur in freshwater lakes, streams, rivers, and in caves with freshwater. The origin of the family appears to be from marine ancestors from the Pacific invading streams in Chile about 75 mya radiating both in Chile and again on the eastern side of the Andes, particularly in Brazil. Of the 63 species, 23 or 36.5% are considered under threat and are in need of conservation action. Guest editors: E. V. Balian, C. Lévêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Global diversity of shrimps (Crustacea: Decapoda: Caridea) in freshwater

Freshwater caridean shrimps account for approximately a quarter of all described Caridea, numerically dominated by the Atyidae and Palaemonidae. With the exception of Antarctica, freshwater shrimp are present in all biogeographical regions. However, the Oriental region harbours the majority of species, whilst the Nearctic and western Palaearctic are very species-poor. Many species are important components of subsistence fisheries, whilst the Giant River Prawn forms the basis of an extensive aquaculture industry. A total of 13 species are threatened or endangered, with one species formally extinct. Guest editors: E. V. Balian, C. Lévêque, H. Segers and K. Martens Freshwater Animal Diversity Assessment     

Geometric morphometric analysis of the freshwater prawn Macrobrachium borellii (Decapoda: Palaemonidae) at a microgeographical scale in a floodplain system

Morphometric studies are useful for delineating the shapes of various populations and species over geographical ranges and as evidence of regional differences in crustaceans. Hydrological fluctuations in a floodplain system modulate the dispersal and presence of decapods among habitats and constitute an important macrofactor that regulate other environmental variables and which could explain the richness, distribution and abundance of organisms that live in these systems. Morphological variations among populations of the freshwater prawn Macrobrachium borellii in a floodplain system at a microgeographical scale were studied using geometric morphometrics. Carapace structure was represented using 16 digitised landmarks. Allometry and sexual dimorphism was tested. Variation in shape was explored via Principal Component Analysis. Canonical Variate Analyses was applied to compare the differences in shape between species’ populations. The correlations and covariations among shapes and hydrometric level, current velocity, geographical location and hydrologic distances were analysed. The average carapace shape was different between sexes in all sites. Populations that were near each other in terms of hydrological distance had similar shapes, but all of the populations differed in shape from the farthest population. The environmental variables were not good predictors of the carapace shape. Instead, the shape was strongly related to the hydrologic distance and geographical location. The swimming characteristics of these prawns and their passive movements, together with the dynamics of a floodplain system, explain the low morphological variation between populations in this study. The dynamic characteristics of the system influence the dispersal of the prawns and allow populations to remain connected.     

Molecular phylogenetics of Kosteletzkya (Malvaceae,Hibisceae) reveals multiple independent and successive polyploid speciation events

Kosteletzkya s.s. is a genus of 17 species (excluding the endemic species of Madagascar), found in the New World, continental Africa, Madagascar, and Southeast Asia. Recent chromosome counts revealed diploid, tetraploid, and hexaploid species. To estimate the history of the genus, we sequenced nuclear and plastid loci for nearly all Kosteletzkya spp., in the majority of cases, with multiple accessions per species. The African species form a paraphyletic grade relative to a New World clade. Polyploidy has occurred only in some African species, resulting in the relatively ancient formation of one putative autotetraploid species (K. semota), one recent allotetraploid species (K. borkouana), two relatively ancient allotetraploid species (K. begoniifolia and K. rotundalata) and one recent allohexaploid species (K. racemosa). Our inferences regarding the hypothesized parentage of the polyploids mostly corroborate previous work based on chromosome‐pairing patterns in artificial hybrids, highlighting the utility of these complementary data sources. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 421–435.     

Phylogenetic evidence for multiple invasions and speciation in caves: the Australian planthopper genus Solonaima (Hemiptera: Fulgoromorpha: Cixiidae)

Abstract. The Australian genus Solonaima comprises thirteen described plus two undescribed species. Six are cavernicolous, obligate or not, and are found in different caves. The phylogeny presented here confirms the monophyly of the genus. This phylogeny was compared with the estimate obtained using the method of Marques and Gnaspini, who recommend coding characters susceptible to parallelism differently from the others. Further comparison was made with a cladogram derived from the matrix from which such characters susceptible to parallelism were withdrawn. Scenarios concerning historical invasions of caves were tested using phylogenetic inference. The most-parsimonious hypothesis proposed four invasions of the caves, within two of which a diversification of species took place.     

The freshwater palaemonid prawns (Crustacea: Decapoda: Caridea) of Myanmar

The taxonomy of the palaemonid freshwater prawns of Myanmar is reviewed and 19 species are recorded. These belong to three genera, with 17 species of Macrobrachium, one species of Palaemonetes and one species of Leptocarpus. The identities of Palaemon spinipes birmanicus Schenkel, 1902, and Palaemon naso Kemp, 1918, are clarified with both recognised as distinct taxa. The taxonomy of several poorly known species of Macrobrachium,viz. M. villosimanus (Tiwari, 1949), M. peguense (Tiwari, 1952), M. hendersoni (De Man, 1906) and M. platyrostrum (Tiwari, 1952) is revised and discussed. Five species are reported from Myanmar for the first time, viz. Macrobrachium lamarrei (H. Milne-Edwards, 1837), M. dayanum (Henderson, 1893), M. lanchesteri (De Man, 1911), M. nipponense (De Haan, 1894), and Palaemonetes sinensis (Sollaud, 1911). One new species, Macrobrachium lanatum, which is closely allied to M. scabriculum (Heller, 1862) and M. dolichodactylus (Hilgendorf, 1879), is described and figured.     

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background

Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog.

Results

Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal.

Conclusions

Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation.     

Multiple drivers of decline in the global status of freshwater crayfish (Decapoda: Astacidea)

Rates of biodiversity loss are higher in freshwater ecosystems than in most terrestrial or marine ecosystems, making freshwater conservation a priority. However, prioritization methods are impeded by insufficient knowledge on the distribution and conservation status of freshwater taxa, particularly invertebrates. We evaluated the extinction risk of the world''s 590 freshwater crayfish species using the IUCN Categories and Criteria and found 32% of all species are threatened with extinction. The level of extinction risk differed between families, with proportionally more threatened species in the Parastacidae and Astacidae than in the Cambaridae. Four described species were Extinct and 21% were assessed as Data Deficient. There was geographical variation in the dominant threats affecting the main centres of crayfish diversity. The majority of threatened US and Mexican species face threats associated with urban development, pollution, damming and water management. Conversely, the majority of Australian threatened species are affected by climate change, harvesting, agriculture and invasive species. Only a small proportion of crayfish are found within the boundaries of protected areas, suggesting that alternative means of long-term protection will be required. Our study highlights many of the significant challenges yet to come for freshwater biodiversity unless conservation planning shifts from a reactive to proactive approach.     

Growth and reproduction in the freshwater crab, Potamon fluviatile (Decapoda, Brachyura)

SUMMARY. 1. The patterns of relative and absolute growth and the reproductive biology of the freshwater crab Potamon fluviatile were studied in a natural population inhabiting a hill stream close to Florence, Italy, over an annual cycle. Periodical inspections of a stretch of the stream were made and morphological and anatomical analysis carried out.
2. As in other decapods, the females are smaller than the males (they can however occasionally reach larger dimensions). This may be determined by a lengthening of the moulting interval in the females, by their higher energetic cost of reproduction (since reproduction occurs simultaneously with moulting, at least in this habitat) and/or by a higher mortality rate resulting from the risks associated with carrying eggs and vagility.
3. The analysis of relative growth in secondary sexual characters (abdomen width and major chela length) with respect to carapace length, shows that the pre-puberty and puberty ecdysis occur at 15 and 35 mm carapace length respectively, which was also confirmed by the gonad weight, vas deferens in males, and the onset of vitellogencsis in females.
4. A delay between anatomical and functional (i.e. the ability to copulate successfully) maturity was observed in the males. Being larger may be an advantage in intra-sexual competition for mating, but larger males, being more vagile, are also more likely to meet receptive females. The females may mate before their puberty moult and store sperms in their seminal receptacles for when they attain full maturity; this could be adaptive since opportunities of encountering males are few and far between in their adult phase, characterized by their vagile and amphibious habits.     

Amplification of multiple copies of mitochondrial Cytochrome b gene fragments in the Australian freshwater crayfish,Cherax destructor Clark (Parastacidae: Decapoda)

Non-coding copies of fragments of the mitochondrial genome translocated to the nucleus or pseudogenes are being found with increasing frequency in a diversity of organisms. As part of a study to evaluate the utility of a range of mitochondrial gene regions for population genetic and systematic studies of the Australian freshwater crayfish, Cherax destructor (the yabby), we report the first detection of Cytochrome b (Cyt b) pseudogenes in crustaceans. We amplified and sequenced fragments of the mitochondrial Cyt b gene from 14 individuals of C. destructor using polymerase chain reaction (PCR) with primers designed from conserved regions of Penaeus monodon and Drosophila melanogaster mitochondrial genomes. The phylogenetic tree produced from the amplified fragments using these primers showed a very different topology to the trees obtained from sequences from three other mitochondrial genes, suggesting one or more nuclear pseudogenes have been amplified. Supporting this conclusion, two highly divergent sequences were isolated from each of two single individuals, and a 2 base pair (bp) deletion in one sequence was observed. There was no evidence to support inadvertent amplification of parasite DNA or contamination of samples from other sources. These results add to other recent observations of pseudogenes suggesting the frequent transfer of mitochondrial DNA (mtDNA) genes to the nucleus and reinforces the necessity of great care in interpreting PCR-generated Cyt b sequences used in population or evolutionary studies in freshwater crayfish and crustaceans more generally.     

Multiple invasions into freshwater by pufferfishes (teleostei: tetraodontidae): a mitogenomic perspective

Pufferfishes of the Family Tetraodontidae are the most speciose group in the Order Tetraodontiformes and mainly inhabit coastal waters along continents. Although no members of other tetraodontiform families have fully discarded their marine lives, approximately 30 tetraodontid species spend their entire lives in freshwaters in disjunct tropical regions of South America, Central Africa, and Southeast Asia. To investigate the interrelationships of tetraodontid pufferfishes and thereby elucidate the evolutionary origins of their freshwater habitats, we performed phylogenetic analysis based on whole mitochondrial genome sequences from 50 tetraodontid species and closely related species (including 31 newly determined sequences). The resulting phylogenies reveal that the family is composed of four major lineages and that freshwater species from the different continents are independently nested in two of the four lineages. A monophyletic origin of the use of freshwater habitats was statistically rejected, and ancestral habitat reconstruction on the resulting tree demonstrates that tetraodontids independently entered freshwater habitats in different continents at least three times. Relaxed molecular-clock Bayesian divergence time estimation suggests that the timing of these invasions differs between continents, occurring at 0-10 million years ago (MA) in South America, 17-38 MA in Central Africa, and 48-78 MA in Southeast Asia. These timings are congruent with geological events that could facilitate adaptation to freshwater habitats in each continent.     

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River

Freshwater fish evolved from anadromous ancestors can be found in almost all continents. The roles of paleogeographic events and nature selection in speciation process often are under focus of research. We studied genetic diversity of anadromous and resident tapertail anchovies (Coilia nasus species complex) in the Yangtze River Basin using 4,434 nuclear loci, and tested the history of freshwater invasion of C. nasus. We found that both C. brachygnathus and C. nasus were valid species, but the resident C. nasus taihuensis and the anadromous C. nasus were not different genetically based on Bayes factor species delimitation (BFD*). Maximum likelihood tree, Network, PCA and STRUCTURE analyses all corroborated the results of BFD*. Two independent freshwater invasion events of C. nasus were supported, with the first event occurring around 4.07 Ma and the second happened around 3.2 Ka. The time of the two freshwater invasions is consistent with different paleogeographic events. Estimation showed that gene flow was higher within ecotypes than between different ecotypes. F‐DIST analyses identified 120 disruptive outliers by comparing C. brachygnathus to anadromous C. nasus, and 21 disruptive outliers by comparing resident C. nasus to anadromous C. nasus. Nine outliers were found to be common between the two comparisons, indicating that independent freshwater invasion of C. nasus might involve similar molecular pathways. The results of this study suggest that adaptation to landlocked freshwater environment of migratory fish can evolve multiple times independently, and morphology of landlocked ecotypes may cause confusion in their taxonomy.     

Phylogeography of the widespread Australian freshwater prawn, Macrobrachium australiense (Decapoda, Palaemonidae)

Aim To investigate the phylogeographic structure of the widespread freshwater prawn, Macrobrachium australiense, within and between major Australian drainage basins using mitochondrial sequence data. This will enable the investigation of historical connections between major drainages and examination of hypotheses of biogeographic associations among Australian freshwater basins. Location Inland, eastern and northern Australia. Methods Sequencing 16S rRNA and ATPase 6 protein coding mitochondrial DNA genes from M. australiense from 19 locations from inland, eastern and northern Australia. Results Within drainage basins, haplotype trees are monophyletic, with the exception of the Finke River from the Lake Eyre Basin. Macrobrachium australiense from the two main inland drainages, the Murray–Darling and Lake Eyre Basin are divergent from each other and do not form a monophyletic group, instead the Murray–Darling Basin haplotypes clade with eastern coastal haplotypes. Haplotypes from neighbouring eastern coastal drainages were found to be quite divergent from each other. Main conclusions The phylogeographic relationships among M. australiense suggest that the two major inland drainages, the Murray–Darling Basin and the Lake Eyre Basin, are not biogeographically closely associated to each other. Instead the Murray–Darling Basin is more closely allied with the eastern coastal drainages across the Great Dividing Range. Despite their proximity the neighbouring southeast Queensland coastal Mary and Brisbane Rivers are also biogeographically divergent from each other. The results also indicate that the Finke River appears to have been isolated from the remainder of the Lake Eyre Basin catchment for a significant period of time.     

DNA taxonomy of the potamid freshwater crabs from Northern Africa (Decapoda,Potamidae)

The Mediterranean area, from southern Balkans to western Maghreb, is inhabited by the Potamon subgenus Euthelphusa, with three currently recognised species. The Maghrebian species P. (E.) algeriense is isolated from other Potamon species by the Mediterranean Sea and the Sahara Desert, and nearly no molecular data are currently available for this taxon. Present study investigated the mtDNA and nuDNA diversity in Potamon algeriense s.l. with the aims of exploring its molecular diversity pattern throughout its known distribution range, and testing the possible presence of cryptic taxa currently lumped under this binomen. The phylogenetic and DNA taxonomy analyses showed the presence of two well-supported clades of species rank within P. algeriense s.l, with an eastern clade including the populations from Tunisia and Numidia, and a western, highly structured clade including the populations from central Algeria and Morocco. In agreement with a typical Maghrebian biogeographic pattern, the distribution of these two species shows a clear east–west divide, with a disjunction zone located in Kabylia, and a strong link between molecular diversity and segregation within different hydrographical basins is evident. The Maghreb thus proved to host an unexpectedly high genetic diversity of, and to constitute a biodiversity hot-spot for, the Potamon subgenus Euthelphusa. In the light of the existence of two well-characterised species currently lumped under P. algeriense s.l., and of their noteworthy molecular structuring, the status of Maghrebian Potamon populations should be re-assessed for both the species present in the area, which are to be considered as independent management units.