There has hitherto been little research into evolutionary and taxonomic relationships amongst species of the freshwater prawn genus Macrobrachium Bate across its global distribution. Previous work by the authors demonstrated that the endemic Australian species did not evolve from a single ancestral lineage. To examine whether other regional Macrobrachium faunas also reflect this pattern of multiple origins, the phylogeny of 30 Macrobrachium species from Asia, Central/South America and Australia was inferred from mitochondrial 16S rRNA sequences. Phylogenetic relationships demonstrate that, despite some evidence for regional diversification, Australia, Asia and South America clearly contain Macrobrachium species that do not share a common ancestry, suggesting that large‐scale dispersal has been a major feature of the evolutionary history of the genus. The evolution of abbreviated larval development (ALD), associated with the transition from an estuarine into a purely freshwater lifecycle, was also mapped onto the phylogeny and was shown to be a relatively homoplasious trait and not taxonomically informative. Other taxonomic issues, as well as the evolutionary origins of Macrobrachium, are also discussed.

In some arid, semi-arid or Mediterranean climate regions, increased water extraction combined with climate change will prolong periods of drought in non-perennial streams, but the effects on macroinvertebrate populations are poorly understood. Drought refuges allow species to survive drying but their use depends on species’ traits, and refuge availability depends on landscape structure. This review evaluates the utility of existing ecological concepts for predicting the role of drought refuges for sustaining biodiversity in non-perennial streams. We also suggest traits that may determine invertebrate species’ resistance or resilience to prolonged drying. Parts of the likely responses by populations to increased stream drying are described by existing ecological concepts, such as the biological traits of species and their interaction with the habitat templet, barriers to dispersal and metapopulation dynamics, the use of drought refuges, habitat fragmentation and population and landscape genetics. However, the limited knowledge of invertebrate life histories in non-perennial streams restricts our ability to use these concepts in a predictive manner. In particular, reach or pool occupancy by species cannot be accurately predicted, but such predictions are necessary for evaluating potential management actions such as the use of environmental flows to sustain drought refuges during dry periods.

BackgroundSome of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics.ResultsWe generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches.ConclusionsWe present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and more generally for other related fish species of the family Pomacentridae.

A detailed study of electrophoretic, morphological and habitat variation amongst species of Cherax in south-western Australia supported the recognition of only five of the eight species currently recognised and revealed that morphological and habitat variation within these crayfish is more extensive and complicated than was previously realised. Within several species morphological and habitat variation was found to be as great as that between species. Furthermore, a major component of the morphological variability, both within and between species, was found to be associated with habitat variation. Three of the five species of Cherax recognised in this study correspond to the consistently recognised and widespread species, C. preissii Erichson, C. quinquecarinatus (Gray) and C. tenuimanus Smith. The two other species are C. crassimantus Riek and C. glaber Riek which have restricted distributions in the extreme south-west of Western Australia. The species C. glabrimanus Riek and C. neocarinatus Riek could not be distinguished from C. quinquecarinatus, nor could C. plebejus (Hess) be distinguished from C. preissii. On a general level, the results of this study question the value of morphological information in systematic studies of freshwater crayfish. Morphologically based taxonomic studies of freshwater crayfish need to be interpreted with caution because, firstly, taxonomic characters may be far more variable than realised; secondly, morphological and habitat differences cannot necessarily be equated with specific distinctions; and thirdly, genetically distinct species that occupy similar habitats need not be morphologically distinct.