Convergent copy number increase of genes associated with freshwater colonization in fishes

Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB8a) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.

Sweet or salty? The origin of freshwater gastrotrichs (Gastrotricha, Chaetonotida) revealed by molecular phylogenetic analysis

Chaetonotidae is the most diverse and widely distributed family of the order Chaetonotida (Gastrotricha) and includes both marine and freshwater species. Although the family is regarded as a sister taxon to the exclusively marine Xenotrichulidae, the type of environment, marine or freshwater, where Chaetonotidae originated is still not known. Here, we reconstructed the phylogeny of the family based on molecular sequence data and mapped both morphological and ecological characters to determine the ancestral environment of the first members of the family. Our results revealed that the freshwater genus Bifidochaetus is the earliest branching lineage in the paraphyletic Chaetonotidae (encompassing Dasydytidae and Neogosseidae). Moreover, we reconstructed Lepidochaetus-Cephalionotus clade as a monophyletic sister group to the remaining chaetonotids, which supports Kisielewski's morphological based hypothesis concerning undifferentiated type of body scales as a most primary character in Chaetonotidae. We also found that reversals to marine habitats occurred independently in different Chaetonotidae lineages, thus marine species in the genera Heterolepidoderma, Halichaetonotus, Aspidiophorus and subgenera Chaetonotus (Schizochaetonotus) or Chaetonotus (Marinochaetus) should be assumed as having secondarily invaded the marine environment. Character mapping revealed a series of synapomorphies that define the clade that includes Chaetonotidae (with Dasydytidae and Neogosseidae), the most important of which may be those linked to reproduction.

Elevated river discharge enhances the immigration of juvenile catadromous and amphidromous fishes into temperate coastal rivers

Anthropogenic alterations to river flow regimes threaten freshwater biodiversity globally, with potentially disproportionate impacts on species that rely on flow cues to trigger critical life history processes, such as migration for diadromous fishes. This study investigates the influence of river discharge on the abundance of juvenile fish moving into rivers by four temperate catadromous or amphidromous species (common galaxias Galaxias maculatus, spotted galaxias Galaxias truttaceus, climbing galaxias Galaxias brevipinnis and the threatened Australian grayling Prototroctes maraena). Fyke netting or fishway trapping was used to catch juvenile fish moving from estuaries into freshwater in five coastal waterways in south-eastern Australia during the spring migratory period. There was a positive relationship between the probability of high catch rates and mean discharge in September. We also found a positive relationship between discharge and the number of recruits captured 22-30 days later in a flow stressed system. In addition, day-of-year had a strong influence on catch rates, with the peak abundance of juveniles for three species most likely to occur midway through the sampling period (spotted galaxias in October, climbing galaxias in late October and Australian grayling in late October and early November). Our study shows that higher magnitudes of river discharge were associated with increased catches of juvenile catadromous and amphidromous fishes. With a limited supply of environmental water, environmental flows used to enhance immigration of these fishes may be best targeted to maintain small amounts of immigration into freshwater populations in waterways or years when discharges are low and stable. When there are natural, large discharge volumes, relatively large numbers of juvenile fish can be expected to enter coastal waterways and during these times environmental flows may not be required to promote immigration.

Profilicollis chasmagnathi (Acanthocephala) parasitizing freshwater fishes: paratenicity and an exception to the phylogenetic conservatism of the genus?

Polymorphid acanthocephalans are parasites of marine mammals, waterfowl and ichthyophagous birds. Among these, the genus Profilicollis is known to use exclusively decapods as intermediate hosts. Here, we report the first record of living cystacanths of Profilicollis parasitizing the body cavity of a fish host, Oligosarcus jenynsii, inhabiting the freshwater section of an estuarial system, Mar Chiquita coastal lagoon, in south-east Buenos Aires Province, Argentina. In this environment, cystacanths of Profilicollis chasmagnathi have been previously recorded infecting decapod crabs and as transient accidental infections in the gut of some carcinophagous fishes. In the present study, larvae from the crab Neohelice granulata, from the intestine of the estuarine fish Odontesthes argentinensis and from the body cavity of O. jenynsii were morphologically and genetically compared, confirming their identity as P. chasmagnathi, a species characteristic of estuaries and marine coasts along Argentina, Uruguay and Chile. These findings can be interpreted as a possible case of incipient paratenicity for Profilicollis, and a colonization event of freshwater habitats, probably promoted by the highly variable conditions, typical of ecotonal environments. In addition, cystacanths of the genus Polymorphus were also found in O. jenynsii, representing the first record of this genus in Oligosarcus from Argentina.

Revisiting Australian Ectocarpus subulatus (Phaeophyceae) From the Hopkins River: Distribution, Abiotic Environment, and Associated Microbiota

In 1995 a strain of Ectocarpus was isolated from Hopkins River Falls, Victoria, Australia, constituting one of few available freshwater or nearly freshwater brown algae, and the only one belonging to the genus Ectocarpus. It has since been used as a model to study acclimation and adaptation to low salinities and the role of its microbiota in these processes. To provide more background information on this model, we assessed if Ectocarpus was still present in the Hopkins river 22 years after the original finding, estimated its present distribution, described its abiotic environment, and determined its in situ microbial composition. We sampled for Ectocarpus at 15 sites along the Hopkins River as well as 10 neighboring sites and found individuals with ITS and cox1 sequences identical to the original isolate at three sites upstream of Hopkins River Falls. The salinity of the water at these sites ranged from 3.1 to 6.9, and it was rich in sulfate (1-5 mM). The diversity of bacteria associated with the algae in situ (1312 operational taxonomic units) was one order of magnitude higher than in previous studies of the original laboratory culture, and 95 alga-associated bacterial strains were isolated from algal filaments on site. In particular, species of Planctomycetes were abundant in situ but rare in laboratory cultures. Our results confirmed that Ectocarpus was still present in the Hopkins River, and the newly isolated algal and bacterial strains offer new possibilities to study the adaptation of Ectocarpus to low salinity and its interactions with its microbiome.

Feasting in fresh water: impacts of food concentration on freshwater tolerance and the evolution of food × salinity response during the expansion from saline into fresh water habitats

Saline to freshwater invasions have become increasingly common in recent years. A key hypothesis is that rates of freshwater invasions have been amplified in recent years by increased food concentration, yet this hypothesis has remained unexplored. We examined whether elevated food concentration could enhance freshwater tolerance, and whether this effect evolves following saline to freshwater invasions. We examined physiological response to salinity and food concentration in a 2 × 2 factorial design, using ancestral brackish and freshwater invading populations of the copepod Eurytemora affinis. We found that high food concentration significantly increases low-salinity tolerance. This effect was reduced in the freshwater population, indicating evolution following the freshwater invasion. Thus, ample food could enable freshwater invasions, allowing subsequent evolution of low-salinity tolerance even under food-poor conditions. We also compared effects of food concentration on freshwater survival between two brackish populations from the native range. Impacts of food concentration on freshwater survival differed between the brackish populations, suggesting variation in functional properties affecting their propensity to invade freshwater habitats. The key implication is that high food concentration could profoundly extend range expansions of brackishwater species into freshwater habitats, potentially allowing for condition-specific competition between saline invaders and resident freshwater species.