Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study, we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using micro‐computed tomographic (µCT) scanning and geometric morphometrics, we quantified body shape, size, and vertebral counts of 31 belonid species. We then examined the pattern and tempo of body shape and size evolution using phylogenetic comparative methods. Our results show that transitions from marine to freshwater habitats have altered the adaptive landscape for needlefishes and expanded morphospace relative to marine taxa. We provide further evidence that freshwater taxa attain reduced sizes either through dwarfism (as inferred from axial skeletal reduction) or through developmental truncation (as inferred from axial skeletal loss). We propose that transitions to freshwater habitats produce morphological novelty in response to novel prey resources and changes in locomotor demands. We find that repeated invasions of different habitats have prompted predictable changes in morphology.     

Marine trophic niche use and life history diversity among Arctic charr Salvelinus alpinus in southwestern Greenland

Life history strategies and potential marine niche use of Arctic charr Salvelinus alpinus (n = 237, 84–652 mm, total body length, L_T) were determined during the ice-free season (2012) at three different watercourses in south-western Greenland. All Arctic charr were collected from freshwater habitats. Based on stable isotopes of δ³⁴S, the Arctic charr were categorized as either marine- or freshwater-dependent feeders. The use of time-integrated trophic tracers (stable isotopes of δ¹³C, δ¹⁵N, δ³⁴S) suggested that several trophic groups of Arctic charr operate alongside within each fjord system. The groups suggested were one group that specialized in the marine habitat, in addition to two freshwater resident morphs (small-sized resident and/or large-growing cannibalistic individuals). Stomach contents consisted entirely of freshwater and terrestrial prey (i.e., insects), indicating that marine-dependent feeders also fed in freshwater habitats after return from their marine migration. Growth and maturity patterns further supported variable life history strategies within each watercourse. The life history strategy patterns and marine trophic niche use were consistent across the watercourses along several hundred kilometres of coastline. This study represents the first ecological baseline for partially anadromous populations of Greenland Arctic charr.     

Abbreviation of larval development and extension of brood care as key features of the evolution of freshwater Decapoda

The transition from marine to freshwater habitats is one of the major steps in the evolution of life. In the decapod crustaceans, four groups have colonized fresh water at different geological times since the Triassic, the freshwater shrimps, freshwater crayfish, freshwater crabs and freshwater anomurans. Some families have even colonized terrestrial habitats via the freshwater route or directly via the sea shore. Since none of these taxa has ever reinvaded its environment of origin the Decapoda appear particularly suitable to investigate life‐history adaptations to fresh water. Evolutionary comparison of marine, freshwater and terrestrial decapods suggests that the reduction of egg number, abbreviation of larval development, extension of brood care and lecithotrophy of the first posthatching life stages are key adaptations to fresh water. Marine decapods usually have high numbers of small eggs and develop through a prolonged planktonic larval cycle, whereas the production of small numbers of large eggs, direct development and extended brood care until the juvenile stage is the rule in freshwater crayfish, primary freshwater crabs and aeglid anomurans. The amphidromous freshwater shrimp and freshwater crab species and all terrestrial decapods that invaded land via the sea shore have retained ocean‐type planktonic development. Abbreviation of larval development and extension of brood care are interpreted as adaptations to the particularly strong variations of hydrodynamic parameters, physico‐chemical factors and phytoplankton availability in freshwater habitats. These life‐history changes increase fitness of the offspring and are obviously favoured by natural selection, explaining their multiple origins in fresh water. There is no evidence for their early evolution in the marine ancestors of the extant freshwater groups and a preadaptive role for the conquest of fresh water. The costs of the shift from relative r‐ to K‐strategy in freshwater decapods are traded‐off against fecundity, future reproduction and growth of females and perhaps against size of species but not against longevity of species. Direct development and extension of brood care is associated with the reduction of dispersal and gene flow among populations, which may explain the high degree of speciation and endemism in directly developing freshwater decapods. Direct development and extended brood care also favour the evolution of social systems, which in freshwater decapods range from simple subsocial organization to eusociality. Hermaphroditism and parthenogenesis, which have evolved in some terrestrial crayfish burrowers and invasive open water crayfish, respectively, may enable populations to adapt to restrictive or new environments by spatio‐temporal alteration of their socio‐ecological characteristics. Under conditions of rapid habitat loss, environmental pollution and global warming, the reduced dispersal ability of direct developers may turn into a severe disadvantage, posing a higher threat of extinction to freshwater crayfish, primary freshwater crabs, aeglids and landlocked freshwater shrimps as compared to amphidromous freshwater shrimps and secondary freshwater crabs.     

Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area

We present a survey on the distribution and habitat range of Polynucleobacter necessarius ssp. asymbioticus (PnecC), a numerically and functionally important taxon in the plankton of freshwater systems. We systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km² area, together with ecologically different habitats outside this area. In total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, e.g. in depth (< 10 cm – 171 m) and pH (3.9–8.5). PnecC bacteria were detected by cultivation‐independent methods in all investigated habitats, and their presence was confirmed by cultivation of strains from selected habitats representing the whole studied ecological range. The determined relative abundance of the subspecies ranged from values close to the detection limit of FISH (0.2%) to 67% (average 14.5%), and the highest observed absolute abundance was 5.3 × 10⁶ cells ml^?1. Statistical analyses revealed that the abundance of PnecC bacteria was partially controlled by factors linked to concentrations of humic substances, which support the hypothesis that these bacteria utilize photodegradation products of humic substances. Based on the revealed statistical relationships, an average relative abundance of this subspecies of 20% in global freshwater habitats was extrapolated. Our study provides important implications for the current debate on ubiquity and biogeography in microorganisms.     

True marine and halophilic anoxygenic phototrophic bacteria

Anoxygenic phototrophic bacteria are widely distributed in marine sediments and shallow waters of the coastal zone, where they often form intensely colored mass developments. The phototrophic bacteria have adapted to the whole spectrum of salt concentrations, from freshwater to saturated brines, and it is apparent that individual species have adapted well to particular habitats and mineral salts compositions, both qualitatively and quantitatively. This adaptation is reflected not only in the demand for defined ranges of salt concentrations, but also in the phylogenetic relationships of these bacteria, as established by 16S rDNA sequences. Major phylogenetic branches of purple sulfur bacteria are represented by: (1) marine and extremely halophilic Ectothiorhodospiraceae, (2) truly marine and halophilic Chromatiaceae and (3) freshwater Chromatiaceae, some of which are tolerant to low salt concentrations and are successful competitors in brackish and marine habitats. Quite similarly, salt-dependent green sulfur bacteria form distinct phylogenetic lines. In addition, also among the phototrophic alpha-Proteobacteria (purple nonsulfur bacteria), distinct phylogenetic lines of salt-dependent species are recognized. Available data give rise to the assumption that salt concentrations of natural habitats are an important selective factor that determines the development of a selected range of phototrophic bacteria in an exclusive way. As a consequence, the salt responses of these bacteria are reflected in their phylogenetic relationships.     

Facultative amphidromy involving estuaries in an annual amphidromous fish from a subtropical marginal range

Variation in the life cycle of diadromous fishes can be explained by differential food availability between marine and freshwater habitats, since migration is often interpreted as a mechanism for exploiting food resources. Theoretically, a migration pattern of mainly remaining in freshwater occurs in tropical and subtropical habitats where fluvial productivity possibly exceeds marine productivity. However, in Yakugachi River, Amami-Oshima Island, southern Japan, low nutrient concentrations in the river suggest that food availability is limited for the subtropical Ryukyu-ayu Plecoglossus altivelis ryukyuensis. Since Ryukyu-ayu is an amphidromous fish that mainly grows in rivers after spending 2 months in the sea, limited food availability in rivers would force this species to migrate to other habitats with better food availability. Otolith increment and Sr:Ca analyses of 48 adult Ryukyu-ayu collected from the Yakugachi River revealed that all individuals visited estuaries more than three times after moving upstream. Although the specific growth rates of this species in the river had no correlation with the salinity profile in the fluvial period, this movement may be an adaptive choice because the salinity profile significantly affected the body size at maturity. Our results highlighted individual-based variations in amphidromous migration for utilizing estuaries, which could be explained by relatively higher productivity in estuarine than in freshwater and marine habitats.     

Salt tolerance and polyphyly in the cyanobacterium Chroococcidiopsis (Pleurocapsales)

Chroococcidiopsis Geitler (Geitler 1933) is a genus of cyanobacteria containing desiccation and radiation resistant strains. Members of the genus live in habitats ranging from hot and cold deserts to fresh and saltwater environments. Morphology and cell division pattern have historically been used to define the genus. To better understand the evolution and ability of the Chroococcidiopsis genus to survive in diverse environments we investigated how salt tolerance varies among 15 strains previously isolated from different locations, and if salt tolerant strains are monophyletic to those isolated from freshwater and land environments. Four markers were sequenced from these 15 strains, the 16S rRNA, rbcL, desC1, and gltX genes. Phylogenetic trees were generated which identified a distinct clade of salt‐tolerant strains. This study demonstrates that the genus is polyphyletic based on saltwater and freshwater phenotypes. To understand the resistance to salt in more details, the strains were grown on a range of sea salt concentrations which demonstrated that the freshwater strains were salt‐intolerant whilst the saltwater strains required salt for growth. This study shows an increased resolution of the phylogeny of Chroococcidiopsis and provides further evidence that the genus is polyphyletic and should be reclassified to improve clarity in the literature.     

DO FRESHWATER FISHES DIVERSIFY FASTER THAN MARINE FISHES? A TEST USING STATE‐DEPENDENT DIVERSIFICATION ANALYSES AND MOLECULAR PHYLOGENETICS OF NEW WORLD SILVERSIDES (ATHERINOPSIDAE)

Freshwater habitats make up only ～0.01% of available aquatic habitat and yet harbor 40% of all fish species, whereas marine habitats comprise >99% of available aquatic habitat and have only 60% of fish species. One possible explanation for this pattern is that diversification rates are higher in freshwater habitats than in marine habitats. We investigated diversification in marine and freshwater lineages in the New World silverside fish clade Menidiinae (Teleostei, Atherinopsidae). Using a time‐calibrated phylogeny and a state‐dependent speciation–extinction framework, we determined the frequency and timing of habitat transitions in Menidiinae and tested for differences in diversification parameters between marine and freshwater lineages. We found that Menidiinae is an ancestrally marine lineage that independently colonized freshwater habitats four times followed by three reversals to the marine environment. Our state‐dependent diversification analyses showed that freshwater lineages have higher speciation and extinction rates than marine lineages. Net diversification rates were higher (but not significant) in freshwater than marine environments. The marine lineage‐through time (LTT) plot shows constant accumulation, suggesting that ecological limits to clade growth have not slowed diversification in marine lineages. Freshwater lineages exhibited an upturn near the recent in their LTT plot, which is consistent with our estimates of high background extinction rates. All sequence data are currently being archived on Genbank and phylogenetic trees archived on Treebase.     

Ecological consequences of invasion across the freshwater–marine transition in a warming world

The freshwater–marine transition that characterizes an estuarine system can provide multiple entry options for invading species, yet the relative importance of this gradient in determining the functional contribution of invading species has received little attention. The ecological consequences of species invasion are routinely evaluated within a freshwater versus marine context, even though many invasive species can inhabit a wide range of salinities. We investigate the functional consequences of different sizes of Corbicula fluminea—an invasive species able to adapt to a wide range of temperatures and salinity—across the freshwater–marine transition in the presence versus absence of warming. Specifically, we characterize how C. fluminea affect fluid and particle transport, important processes in mediating nutrient cycling (NH₄‐N, NO₃‐N, PO₄‐P). Results showed that sediment particle reworking (bioturbation) tends to be influenced by size and to a lesser extent, temperature and salinity; nutrient concentrations are influenced by different interactions between all variables (salinity, temperature, and size class). Our findings demonstrate the highly context‐dependent nature of the ecosystem consequences of invasion and highlight the potential for species to simultaneously occupy multiple components of an ecosystem. Recognizing of this aspect of invasibility is fundamental to management and conservation efforts, particularly as freshwater and marine systems tend to be compartmentalized rather than be treated as a contiguous unit. We conclude that more comprehensive appreciation of the distribution of invasive species across adjacent habitats and different seasons is urgently needed to allow the true extent of biological introductions, and their ecological consequences, to be fully realized.     

Biogeography,habitat transitions and hybridization in a radiation of South American silverside fishes revealed by mitochondrial and genomic RAD data

Rivers and lake systems in the southern cone of South America have been widely influenced by historical glaciations, carrying important implications for the evolution of aquatic organisms, including prompting transitions between marine and freshwater habitats and by triggering hybridization among incipient species via waterway connectivity and stream capture events. Silverside fishes (Odontesthes) in the region comprise a radiation of 19 marine and freshwater species that have been hypothesized on the basis of morphological or mitochondrial DNA data to have either transitioned repeatedly into continental waters from the sea or colonized marine habitats following freshwater diversification. New double digest restriction‐site associated DNA data presented here provide a robust framework to investigate the biogeographical history of and habitat transitions in Odontesthes. We show that Odontesthes silversides originally diversified in the Pacific but independently colonized the Atlantic three times, producing three independent marine‐to‐freshwater transitions. Our results also indicate recent introgression of marine mitochondrial haplotypes into two freshwater clades, with more recurring instances of hybridization among Atlantic‐ versus Pacific‐slope species. In Pacific freshwater drainages, hybridization with a marine species appears to be geographically isolated and may be related to glaciation events. Substantial structural differences of estuarine gradients between these two geographical areas may have influenced the frequency, intensity and evolutionary effects of hybridization events.     

Out of the blue: adaptive visual pigment evolution accompanies Amazon invasion

Incursions of marine water into South America during the Miocene prompted colonization of freshwater habitats by ancestrally marine species and present a unique opportunity to study the molecular evolution of adaptations to varying environments. Freshwater and marine environments are distinct in both spectra and average intensities of available light. Here, we investigate the molecular evolution of rhodopsin, the photosensitive pigment in the eye that activates in response to light, in a clade of South American freshwater anchovies derived from a marine ancestral lineage. Using likelihood-based comparative sequence analyses, we found evidence for positive selection in the rhodopsin of freshwater anchovy lineages at sites known to be important for aspects of rhodopsin function such as spectral tuning. No evidence was found for positive selection in marine lineages, nor in three other genes not involved in vision. Our results suggest that an increased rate of rhodopsin evolution was driven by diversification into freshwater habitats, thereby constituting a rare example of molecular evolution mirroring large-scale palaeogeographic events.     

Biomass production and energy source of thermophiles in a Japanese alkaline geothermal pool

Microbial biomass production has been measured to investigate the contribution of planktonic bacteria to fluxations in dissolved organic matter in marine and freshwater environments, but little is known about biomass production of thermophiles inhabiting geothermal and hydrothermal regions. The biomass production of thermophiles inhabiting an 85°C geothermal pool was measured by in situ cultivation using diffusion chambers. The thermophiles' growth rates ranged from 0.43 to 0.82 day^?1, similar to those of planktonic bacteria in marine and freshwater habitats. Biomass production was estimated based on cellular carbon content measured directly from the thermophiles inhabiting the geothermal pool, which ranged from 5.0 to 6.1 μg C l^?1 h^?1. This production was 2–75 times higher than that of planktonic bacteria in other habitats, because the cellular carbon content of the thermophiles was much higher. Quantitative PCR and phylogenetic analysis targeting 16S rRNA genes revealed that thermophilic H₂‐oxidizing bacteria closely related to Calderobacterium and Geothermobacterium were dominant in the geothermal pool. Chemical analysis showed the presence of H₂ in gases bubbling from the bottom of the geothermal pool. These results strongly suggested that H₂ plays an important role as a primary energy source of thermophiles in the geothermal pool.     

Trophic ecology of a freshwater sponge (Spongilla lacustris) revealed by stable isotope analysis

The vital roles that sponges play in marine habitats are well-known. However, sponges inhabiting freshwaters have been largely ignored despite having widespread distributions and often high local abundances. We used natural abundance stable isotope signatures of carbon and nitrogen (δ ¹³C and δ ¹⁵N) to infer the primary food source of the cosmopolitan freshwater sponge Spongilla lacustris. Our results suggest that S. lacustris feed largely on pelagic resources and may therefore link pelagic and benthic food webs. A facultative association between S. lacustris and endosymbiotic green algae caused S. lacustris to have significantly depleted carbon and nitrogen signatures that may reflect carbon and nitrogen exchange between sponges and their symbiotic algae. Isotopic data from specialist sponge consumers demonstrated that sponges hosting zoochlorellae were the major component of the diet of the spongillafly Climacia areolaris and the sponge-eating caddisfly Ceraclea resurgens suggesting that the symbiosis between freshwater sponges and algae is important to sponge predator trophic ecology. Our results help define the role of sponges in freshwater ecosystems and shed new light on the evolution and ecological consequences of a complex tri-trophic symbiosis involving freshwater sponges, zoochlorellae, and spongivorous insects.     

Field studies of ammonia excretion in Aphanius iberus (Pisces; Cyprinodontidae): body size and habitat effects

The effects of body size and habitat variability on ammonia excretion rates (R_AMs) of Aphanius iberus were analyzed in situ for the first time. At hourly intervals during a 5‐h field experiment, ammonia excretion was measured in 75 mature specimens from three sampling sites (small creek, marine salt‐mine, and salt‐marsh) established in a gradient of water salinity (0–5; 35–40; 65–70‰). Our results showed a specific size dependence pattern of R_AMs in the reproduction period, which might reflect an effect of the reproductive effort. In addition, the results point to a significant decrease in mean R_AM values of each population from freshwater aquatic systems (3.81 ± 0.58 μmol g⁻¹ h⁻¹ in fish of 2.8 ± 0.3 mm total length, TL) to salt aquatic systems with significantly higher alkalinity (2.52 ± 0.35 μmol g⁻¹ h⁻¹ in fish of 3.1 ± 0.5 mm TL in marine salt‐mine; 1.98 ± 0.55 μmol g⁻¹ h⁻¹ in fish of 3.1 ± 0.4 mm TL in salt‐marsh). Due to the size‐dependent pattern, R_AM in different habitats cannot be compared directly; ancova , followed by residual compared analysis (regression‐related techniques), is seen as a valid method for this purpose. This work presents the first field data on ammonia excretion in the Aphanius genus and the flexible physiologic response characteristic of Cyprinodontids has been demonstrated.     

Tracing biogeochemical subsidies from glacier runoff into Alaska's coastal marine food webs

Nearly half of the freshwater discharge into the Gulf of Alaska originates from landscapes draining glacier runoff, but the influence of the influx of riverine organic matter on the trophodynamics of coastal marine food webs is not well understood. We quantified the ecological impact of riverine organic matter subsidies to glacier‐marine habitats by developing a multi‐trophic level Bayesian three‐isotope mixing model. We utilized large gradients in stable (δ¹³C, δ¹⁵N, δ²H) and radiogenic (Δ¹⁴C) isotopes that trace riverine and marine organic matter sources as they are passed from lower to higher trophic levels in glacial‐marine habitats. We also compared isotope ratios between glacial‐marine and more oceanic habitats. Based on isotopic measurements of potential baseline sources, ambient water and tissues of marine consumers, estimates of the riverine organic matter source contribution to upper trophic‐level species including fish and seabirds ranged from 12% to 44%. Variability in resource use among similar taxa corresponded to variation in species distribution and life histories. For example, riverine organic matter assimilation by the glacier‐nesting seabirds Kittlitz's murrelet (Brachyramphus brevirostris) was greater than that of the forest‐nesting marbled murrelet (B. marmoratus). The particulate and dissolved organic carbon in glacial runoff and near surface coastal waters was aged (12100–1500 years BP ¹⁴C‐age) but dissolved inorganic carbon and biota in coastal waters were young (530 years BP ¹⁴C‐age to modern). Thus terrestrial‐derived subsidies in marine food webs were primarily composed of young organic matter sources released from glacier ecosystems and their surrounding watersheds. Stable isotope compositions also revealed a divergence in food web structure between glacial‐marine and oceanic sites. This work demonstrates linkages between terrestrial and marine ecosystems, and facilitates a greater understanding of how climate‐driven changes in freshwater runoff have the potential to alter food web dynamics within coastal marine ecosystems in Alaska.     

Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America

In this study, the competing hypotheses of single vs. double colonisation events for freshwater Pachyurinae (Sciaenidae) in South America is tested and the historical biogeography of the expansion of this clade within the continent is reconstructed based on phylogenetic analysis. Parsimony and Bayesian inference (BI) for 19 marine and freshwater species assigned to Sciaenidae, Haemulidae and Polypteridae were determined based on partial sequences of the mitochondrial 16S and cytochrome b genes and fragments of the nuclear Tmo‐4C4 and rhodopsin genes. A parsimonious ancestral character reconstruction of euryhalinity was performed on a clade of families of closely related fishes to evaluate the role of ecological fitting in the colonisation of freshwater by a marine sciaenid. The parsimony and BI phylogenetic hypotheses for the concatenated sequences supported the monophyly of the freshwater Sciaenidae. Divergence of the two freshwater clades of Sciaenidae, Pachyurinae and Plagioscion, occurred within the Amazon Basin. Within Pachyurinae, two clades were recovered: one composed of species from the Amazon and the Paraná Basin and a second with representatives from the São Francisco and south‐eastern Atlantic basins. The results were compatible with the hypothesis of a single colonisation event of South American freshwater habitats by a marine lineage. The hypothesis of gradual adaptation to freshwater was rejected in favour of the hypothesis of ecological fitting. Sciaenidae, or a subordinate lineage within the family, is ancestrally capable of withstanding exposure to low‐salinity habitats, which putatively facilitated the colonisation of freshwater habitats. The subsequent diversification and expansion of Pachyurinae across South America followed this colonisation and replicated the general pattern of the area relationships of South American river basins for several other fish groups.     

Interactive effects of road salt and sediment disturbance on the productivity of seven common aquatic macrophytes

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