Origin and early evolution of photosynthetic eukaryotes in freshwater environments: reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution

Phylogenetic analyses were performed on concatenated data sets of 31 genes and 11,789 unambiguously alignable characters from 37 cyanobacterial and 35 chloroplast genomes. The plastid lineage emerged somewhat early in the cyanobacterial tree, at a time when Cyanobacteria were likely unicellular and restricted to freshwater ecosystems. Using relaxed molecular clocks and 22 age constraints spanning cyanobacterial and eukaryote nodes, the common ancestor to the photosynthetic eukaryotes was predicted to have also inhabited freshwater environments around the time that oxygen appeared in the atmosphere (2.0–2.3 Ga). Early diversifications within each of the three major plastid clades were also inferred to have occurred in freshwater environments, through the late Paleoproterozoic and into the middle Mesoproterozoic. The colonization of marine environments by photosynthetic eukaryotes may not have occurred until after the middle Mesoproterozoic (1.2–1.5 Ga). The evolutionary hypotheses proposed here predict that early photosynthetic eukaryotes may have never experienced the widespread anoxia or euxinia suggested to have characterized marine environments in the Paleoproterozoic to early Mesoproterozoic. It also proposes that earliest acritarchs (1.5–1.7 Ga) may have been produced by freshwater taxa. This study highlights how the early evolution of habitat preference in photosynthetic eukaryotes, along with Cyanobacteria, could have contributed to changing biogeochemical conditions on the early Earth.     

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.     

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.     

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.     

Into the deep: new discoveries at the base of the green plant phylogeny

Recent data have provided evidence for an unrecognised ancient lineage of green plants that persists in marine deep-water environments. The green plants are a major group of photosynthetic eukaryotes that have played a prominent role in the global ecosystem for millions of years. A schism early in their evolution gave rise to two major lineages, one of which diversified in the world's oceans and gave rise to a large diversity of marine and freshwater green algae (Chlorophyta) while the other gave rise to a diverse array of freshwater green algae and the land plants (Streptophyta). It is generally believed that the earliest-diverging Chlorophyta were motile planktonic unicellular organisms, but the discovery of an ancient group of deep-water seaweeds has challenged our understanding of the basal branches of the green plant phylogeny. In this review, we discuss current insights into the origin and diversification of the green plant lineage.     

Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny

The cryptomonads is a well-defined lineage of unicellular eukaryotes, composed of several marine and freshwater groups. However, the evolutionary relationships among these groups are unclear due to conflicting inferences between morphological and molecular phylogenies. Here, we have inferred the evolutionary relationships among marine and freshwater species in order to better understand the importance of the marine-freshwater boundary on the historical diversification patterns of cryptomonads. We have constructed improved molecular phylogenies by taking into account rate variation both across sites and across sequences (covarion substitutions), and by analysing the vast majority of publicly available cryptomonad 18S rRNA sequences and related environmental phylotypes. The resulting phylogenies included 55 sequences, and revealed two novel freshwater cryptomonad clades (CRY1 and CRY2) and a large hidden diversity of cryptomonads. CRY1 was placed deeply within the cryptomonad phylogeny together with all the major freshwater lineages (i.e. Goniomonas and Cryptomonas), while CRY2 was placed within a lineage of marine species identified as Plagioselmis-like with the aid of a new sequence generated from a cultured species. The inferred phylogenies suggest only few successful marine-freshwater transitions over the history of cryptomonads. Most of the transitions seem to have occurred from marine to fresh waters, but re-colonizations of marine habitats have also taken place. This implies that the differences in the biogeophysical conditions between marine and fresh waters constitute a substantial barrier for the cross-colonization of these environments by cryptomonads.     

Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation

Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.     

Freshwater habitat use by a moray eel species,Gymnothorax polyuranodon,in Fiji shown by otolith microchemistry

Freshwater eels of the Anguillidae are diadromous because they migrate between ocean and freshwater environments, but other anguilliform fishes are generally considered to be strictly marine species. A few marine eels of the Muraenidae and Ophichthidae have occasionally been found in freshwater or estuaries, indicating that anguillids are not the only anguilliform eels that can use freshwater in some parts of the world. The moray eel Gymnothorax polyuranodon is one species that is known to be present in freshwater in the Indo-Pacific, but its life history is unknown. One way to evaluate what types of habitats are used by fishes is to determine the ratio of strontium (Sr) to calcium (Ca) in their otoliths, because this can show if they have used freshwater or saltwater environments. To evaluate the patterns of freshwater use by this unusual species of marine eel, the otolith Sr/Ca ratios of four G. polyuranodon (275–344 mm) caught in a freshwater stream of Fiji were analyzed. The consistently low Sr/Ca values (0–4) indicated upstream movement after settlement and freshwater or estuarine residence of all four individuals. These eels did not appear to have entered freshwater just for a short time period, which is consistent with other reports that this species is present in estuarine and freshwater habitats. This suggests that G. polyuranodon may be a catadromous species of marine eel. The similarities and differences between the life histories of anguillid eels and the few marine eels that have evolved the ability to invade freshwater habitats is discussed in relation to the evolutionary origin of diadromy in anguilliform fishes that originated in the marine environment.     

Eocene–Oligocene sea-level fall drove amphipod habitat shift from marine to freshwater in the Far East

The Eocene–Oligocene sea-level fall has been viewed as a primary driver of biological succession. We used Anisogammaridae living in both marine and freshwater habitats to test the hypothesis that Eocene–Oligocene sea-level fall can explain the marine–freshwater habitat shift in the Far East. We obtained three mitochondrial and two nuclear fragments for 138 samples representing 31 species, covering marine and freshwater habitats from latitudes 24 to 50°N. The phylogenetic analyses revealed that freshwater Anisogammaridae is monophyletic. Divergence-time estimation and ancestral range reconstruction indicate that the family originated from a marine habitat in the North Pacific region during the Eocene and separated between marine and freshwater lineages at 38 Ma. The freshwater lineage diversified at 27 Ma, and further diverged into lotic and lentic clades. Our results suggest that the Eocene–Oligocene sea-level fall provided an opportunity for marine-derived Anisogammaridae to shift to new freshwater habitats. The freshwater anisogammarids dispersed from north to south, resulting in the restriction of current marine species restricted to the latitudes 35–50°N and the range of freshwater species in latitudes 24–40°N. Deep divergences within the freshwater lineage were related to the separation of lotic and lentic environments and the opening of the Japan Sea.     

Phylogenetic distribution of compatible solute synthesis genes support a freshwater origin for cyanobacteria

Previous work using ancestral state reconstruction of habitat salinity preference proposed that the early cyanobacteria likely lived in a freshwater environment. The aim of this study was to test that hypothesis by performing phylogenetic analyses of the genes underlying salinity preferences in the cyanobacteria. Phylogenetic analysis of compatible solute genes shows that sucrose synthesis genes were likely ancestral in the cyanobacteria, and were also likely inherited during the cyanobacterial endosymbiosis and into the photosynthetic algae and land plants. In addition, the genes for the synthesis of compatible solutes that are necessary for survival in marine and hypersaline environments (such as glucosylglycerol, glucosylglycerate, and glycine betaine) were likely acquired independently high up (i.e., more recently) in the cyanobacterial tree. Because sucrose synthesis is strongly associated with growth in a low salinity environment, this independently supports a freshwater origin for the cyanobacteria. It is also consistent with geologic evidence showing that the early oceans were much warmer and saltier than modern oceans—sucrose synthesis alone would have been insufficient for early cyanobacteria to have colonized early Precambrian oceans that had a higher ionic strength. Indeed, the acquisition of an expanded set of new compatible solute genes may have enabled the historical colonization of marine and hypersaline environments by cyanobacteria, midway through their evolutionary history.     

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.     

Importance of geographic origin for invasion success: A case study of the North and Baltic Seas versus the Great Lakes–St. Lawrence River region

Recently, several studies indicated that species from the Ponto‐Caspian region may be evolutionarily predisposed to become nonindigenous species (NIS); however, origin of NIS established in different regions has rarely been compared to confirm these statements. More importantly, if species from certain area/s are proven to be better colonizers, management strategies to control transport vectors coming from those areas must be more stringent, as prevention of new introductions is a cheaper and more effective strategy than eradication or control of established NIS populations. To determine whether species evolved in certain areas have inherent advantages over other species in colonizing new habitats, we explored NIS established in the North and Baltic Seas and Great Lakes–St. Lawrence River regions—two areas intensively studied in concern to NIS, highly invaded by Ponto‐Caspian species and with different salinity patterns (marine vs. freshwater). We compared observed numbers of NIS in these two regions to expected numbers of NIS from major donor regions. The expected numbers were calculated based on the available species pool from donor regions, frequency of shipping transit, and an environmental match between donor and recipient regions. A total of 281 NIS established in the North and Baltic Seas and 188 in the Great Lakes–St. Lawrence River. Ponto‐Caspian taxa colonized both types of habitats, saltwater areas of the North and Baltic Seas and freshwater of the Great Lakes–St. Lawrence River, in much higher numbers than expected. Propagule pressure (i.e., number of introduced individuals or introduction effort) is of great importance for establishment success of NIS; however in our study, either shipping vector or environmental match between regions did not clarify the high numbers of Ponto‐Caspian taxa in our study areas. Although we cannot exclude the influence of other transport vectors, our findings suggest that the origin of the species plays an important role for the predisposition of successful invaders.     

Diatoms diversify and turn over faster in freshwater than marine environments*

Many clades that span the marine–freshwater boundary are disproportionately more diverse in the younger, shorter lived, and scarcer freshwater environments than they are in the marine realm. This disparity is thought to be related to differences in diversification rates between marine and freshwater lineages. However, marine and freshwaters are not ecologically homogeneous, so the study of diversification across the salinity divide should also account for other potentially interacting variables. In diatoms, freshwater and substrate‐associated (benthic) lineages are several‐fold more diverse than their marine and suspended (planktonic) counterparts. These imbalances provide an excellent system to understand whether these variables interact with diversification. Using multistate hidden‐state speciation and extinction models, we found that freshwater lineages diversify faster than marine lineages regardless of whether they inhabit the plankton or the benthos. Freshwater lineages also had higher turnover rates (speciation + extinction), suggesting that habitat transitions impact speciation and extinction rates jointly. The plankton–benthos contrast was also consistent with state‐dependent diversification, but with modest differences in diversification and turnover rates. Asymmetric and bidirectional transitions rejected hypotheses about the plankton and freshwaters as absorbing, inescapable habitats. Our results further suggest that the high turnover rate of freshwater diatoms is related to high turnover of freshwater systems themselves.     

Red and green algal origin of diatom membrane transporters: insights into environmental adaptation and cell evolution

Membrane transporters (MTs) facilitate the movement of molecules between cellular compartments. The evolutionary history of these key components of eukaryote genomes remains unclear. Many photosynthetic microbial eukaryotes (e.g., diatoms, haptophytes, and dinoflagellates) appear to have undergone serial endosymbiosis and thereby recruited foreign genes through endosymbiotic/horizontal gene transfer (E/HGT). Here we used the diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum as models to examine the evolutionary origin of MTs in this important group of marine primary producers. Using phylogenomics, we used 1,014 diatom MTs as query against a broadly sampled protein sequence database that includes novel genome data from the mesophilic red algae Porphyridium cruentum and Calliarthron tuberculosum, and the stramenopile Ectocarpus siliculosus. Our conservative approach resulted in 879 maximum likelihood trees of which 399 genes show a non-lineal history between diatoms and other eukaryotes and prokaryotes (at the bootstrap value ≥70%). Of the eukaryote-derived MTs, 172 (ca. 25% of 697 examined phylogenies) have members of both red/green algae as sister groups, with 103 putatively arising from green algae, 19 from red algae, and 50 have an unresolved affiliation to red and/or green algae. We used topology tests to analyze the most convincing cases of non-lineal gene history in which red and/or green algae were nested within stramenopiles. This analysis showed that ca. 6% of all trees (our most conservative estimate) support an algal origin of MTs in stramenopiles with the majority derived from green algae. Our findings demonstrate the complex evolutionary history of photosynthetic eukaryotes and indicate a reticulate origin of MT genes in diatoms. We postulate that the algal-derived MTs acquired via E/HGT provided diatoms and other related microbial eukaryotes the ability to persist under conditions of fluctuating ocean chemistry, likely contributing to their great success in marine environments.     

The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages

The recent discovery of a diverse phylogenetic assemblage of picoeukaryotes from environments such as oceans, salt marshes and acidic habitats, has expanded the debates about the extent and origin of microbial eukaryotes. However, the diversity of these eukaryote microorganisms, that overlap bacteria in size, and their environmental and biogeographical ubiquity remains poorly understood. Here we survey picoeukaryotes (microbial eukaryotes of 0.2-5 microm in size) from an oligotrophic (nutrient deficient) freshwater habitat using ribosomal RNA gene sequences. Three taxonomic groups the Heterokonta, Cryptomonads and the Alveolata dominated the detected diversity. Most sequences represented previously unsampled species, with several being unassignable to known taxonomic groups and plausibly represent new or unsampled phyla. Many freshwater phylogenetic groups identified in this study appeared unrelated to picoeukaryotic sequences identified in marine ecosystems, suggesting that aspects of eukaryote microbial diversity are specific to certain aquatic environments. Conversely, at least five phylogenetic clusters comprised sequences from freshwater and globally dispersed and often contrasting environments, supporting the concept that a number of picoeukaryotic lineages are widely distributed.     

Molecular comparisons of freshwater and marine isolates of the same morphospecies of heterotrophic flagellates

Heterotrophic flagellates are key components of all ecosystems. Understanding the patterns of biodiversity of these organisms is thus particularly important. Here we analyzed the intraspecific diversity of 10 morphospecies of heterotrophic flagellates comprising representatives of the Apusozoa (2 morphospecies) and Kinetoplastea (8 morphospecies), all belonging to the most common flagellates with worldwide distribution. Most morphospecies showed a mixing of lineages isolated from diverse habitats, indicating that some lineages of these morphospecies had been able to colonize different habitats several times. Furthermore, our results revealed remarkable levels of genetic divergence within most of the morphospecies studied, underlining the difficulty of correctly determining species by means of morphology alone. Many cryptic or pseudocryptic species seem to occur. Our results revealed clear divergence between marine and freshwater lineages of the morphospecies Ancyromonas sigmoides, showing that freshwater lineages have not been able to colonize marine environments and marine lineages have not been able to colonize freshwater environments for a long time.     

Do saline taxa evolve faster? Comparing relative rates of molecular evolution between freshwater and marine eukaryotes

The major branches of life diversified in the marine realm, and numerous taxa have since transitioned between marine and freshwaters. Previous studies have demonstrated higher rates of molecular evolution in crustaceans inhabiting continental saline habitats as compared with freshwaters, but it is unclear whether this trend is pervasive or whether it applies to the marine environment. We employ the phylogenetic comparative method to investigate relative molecular evolutionary rates between 148 pairs of marine or continental saline versus freshwater lineages representing disparate eukaryote groups, including bony fish, elasmobranchs, cetaceans, crustaceans, mollusks, annelids, algae, and other eukaryotes, using available protein‐coding and noncoding genes. Overall, we observed no consistent pattern in nucleotide substitution rates linked to habitat across all genes and taxa. However, we observed some trends of higher evolutionary rates within protein‐coding genes in freshwater taxa—the comparisons mainly involving bony fish—compared with their marine relatives. The results suggest no systematic differences in substitution rate between marine and freshwater organisms.     

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.