Why are there so few fish in the sea?

Behavioral biomarkers in fishes: A non-lethal approach to assess the effects of chemical pollution on freshwater ecosystems

The expansion of the human population and the escalating use of chemical products pose a considerable threat to aquatic biodiversity. Consequently, there is an imperative need for the implementation of non-lethal, cost-effective, and easily deployable biomonitoring tools. In this context, fish and their behavior as biomarkers have gained prominence in monitoring of freshwater ecosystems. The aim of this study was to assess the state of art in the use of behavioral biomarkers in ecotoxicology, emphasizing their role as informative tools for global environmental monitoring. Through a systematic literature search, ninety-two articles focusing on the evaluation of behavioral changes in freshwater fish in response to pollution were identified. The most prevalent keywords were "behavior" (7%) and "zebrafish" (6%). Experiments were conducted in countries with expansive territories, such as the United States (18%) and Brazil (17%). Exotic species were primarily employed (58%), with Danio rerio (26%) being the most frequently studied species. Among pollutants, pesticides (32%) and medicines (25%) were the most frequently studied, while locomotion (38%) and social behaviors (18%) were the most frequently evaluated behaviors. Across these studies, authors consistently reported significant changes in the behavior of fish exposed to contaminants, including decreased swimming speed and compromised feeding efficiency. The review findings affirm that evaluating behavioral biomarkers in freshwater fish offers an informative, non-lethal, cost-effective, and easily implementable approach to understanding pollution impacts on freshwater ecosystems. Although few studies on behavioral biomarkers were available to date, the number has rapidly increased in recent years. Furthermore, a variety of novel approaches and study models are being included. Research into behavioral biomarkers is crucial for understanding and managing environmental risks in freshwater ecosystems. Nevertheless, further studies are needed to enhance our understanding of behavioral toxicity indicators, considering factors such as life stage, sex, and breeding season in the tested species.

Freshwater Habitats Promote Rapid Rates of Phenotypic Evolution in Sculpin Fishes (Perciformes: Cottoidea)

AbstractInvasions of freshwater habitats by marine fishes provide exceptional cases of habitat-driven biological diversification. Freshwater habitats make up less than 1% of aquatic habitats but contain ∼50% of fish species. However, while the dominant group of freshwater fishes (Otophysi) is older than that of most marine fishes (Percomorphaceae), it is less morphologically diverse. Classically, scientists have invoked differences in the tempo and/or mode of evolution to explain such cases of unequal morphological diversification. We tested for evidence of these phenomena in the superfamily Cottoidea (sculpins), which contains substantial radiations of marine and freshwater fishes. We find that the morphology of freshwater sculpins evolves faster but under higher constraint than that of marine sculpins, causing widespread convergence in freshwater sculpins and more morphological disparity in marine sculpins. The endemic freshwater sculpins of Lake Baikal, Siberia, are exceptions that demonstrate elevated novelty akin to that of marine sculpins. Several tantalizing factors may explain these findings, such as differences in habitat stability and/or habitat connectivity between marine and freshwater systems.

Control of fluid intake in dehydrated rats and evolution of sodium appetite

The objective of the present work is to examine from a new perspective the existence of causal factors not predicted by the classical theory that thirst and sodium appetite are two distinct motivations. For example, we ask why water deprivation induces sodium appetite, thirst is not "water appetite", and intracellular dehydration potentially causes sodium appetite. Contrary to the classical theory, we suggest that thirst first, and sodium appetite second, designate a temporal sequence underlying the same motivation. The single motivation becomes an "intervenient variable" a concept borrowed from the literature, fully explained in the text, between causes of dehydration (extracellular, intracellular, or both together), and respective behavioral responses subserved by hindbrain-dependent inhibition (e.g., lateral parabrachial nucleus) and forebrain facilitation (e.g., angiotensin II). A corollary is homology between rat sodium appetite and marine teleost thirst-like motivation that we name "protodipsia". The homology argument rests on similarities between behavior (salty water intake) and respective neuroanatomical as well as functional mechanisms. Tetrapod origin in a marine environment provides additional support for the homology. The single motivation hypothesis is also consistent with ingestive behaviors in nature given similarities (e.g., thirst producing brackish water intake) between the behavior of the laboratory rat and wild animals, rodents included. The hypotheses of single motivation and homology might explain why hyperosmotic rats, or eventually any other hyperosmotic tetrapod, shows paradoxical signs of sodium appetite. They might also explain how ingestive behaviors determined by dehydration and subserved by hindbrain inhibitory mechanisms contributed to tetrapod transition from sea to land.

Molecular evidence for a new endemic species of Acartia (Copepoda, Calanoida) from the Southeast Pacific coast

The loss of biodiversity in marine populations is one of the consequences of the increased events of extreme environmental conditions in the oceans, which can condition the persistence of populations to future scenarios of climate change. Therefore, it is extremely necessary to explore and monitor the genetic diversity of natural populations. In the Southeast Pacific Ocean (SEPO), specifically on the coast of Chile, the presence of the copepod Acartia tonsa has been indicated solely using morphological evidence, due to the absence of genetic information. In the present work, the genetic diversity, population structure and phylogenetic position within the genus Acartia, of populations identified morphologically as A. tonsa, was evaluated by amplification of the mitochondrial cytochrome c oxidase subunit I and nuclear marker 18 s. Our results showed that the populations identified as A. tonsa correspond to a new monophyletic group endemic to SEPO (GMYC = 1.00; PTP = 0.95). The populations showed moderate to high genetic diversity with an incipient structuring between populations and biogeographic zones. Our results suggest that despite the homogenizing effect of the Humboldt Current, isolation by distance and contrasting environmental conditions at different geographic scales have an important influence on the genetic diversity of zooplankton in the SEPO region.

Effects of the environment on the evolution of the vertebrate urinary tract

Evolution of the vertebrate urinary system occurs in response to numerous selective pressures, which have been incompletely characterized. Developing research into urinary evolution led to the occurrence of clinical applications and insights in paediatric urology, reproductive medicine, urolithiasis and other domains. Each nephron segment and urinary organ has functions that can be contextualized within an evolutionary framework. For example, the structure and function of the glomerulus and proximal tubule are highly conserved, enabling blood cells and proteins to be retained, and facilitating the elimination of oceanic Ca+ and Mg+. Urea emerged as an osmotic mediator during evolution, as cells of large organisms required increased precision in the internal regulation of salinity and solutes. As the first vertebrates moved from water to land, acid-base regulation was shifted from gills to skin and kidneys in amphibians. In reptiles and birds, solute regulation no longer occurred through the skin but through nasal salt glands and post-renally, within the cloaca and the rectum. In placental mammals, nasal salt glands are absent and the rectum and urinary tracts became separate, which limited post-renal urine concentration and led to the necessity of a kidney capable of high urine concentration. Considering the evolutionary and environmental selective pressures that have contributed to renal evolution can help to gain an increased understanding of renal physiology.

Climate change threats to the global functional diversity of freshwater fish

Climate change impacts on freshwater ecosystems and freshwater biodiversity show strong spatial variability, highlighting the importance of a global perspective. While previous studies on biodiversity mostly focused on species richness, functional diversity, which is a better predictor of ecosystem functioning, has received much less attention. This study aims to comprehensively assess climate change threats to the functional diversity of freshwater fish across the world, considering three complementary metrics-functional richness, evenness and divergence. We built on existing spatially explicit projections of geographical ranges for 11,425 riverine fish species as affected by changes in streamflow and water temperature extremes at four warming levels (1.5°C, 2.0°C, 3.2°C and 4.5°C). To estimate functional diversity, we considered the following four continuous, morphological and physiological traits: relative head length, relative body depth, trophic level and relative growth rate. Together, these traits cover five ecological functions. We treated missing trait values in two different ways: we either removed species with missing trait values or imputed them. Depending on the warming level, 6%-25% of the locations globally face a complete loss of functional diversity when assuming no dispersal (6%-17% when assuming maximal dispersal), with hotspots in the Amazon and Paraná River basins. The three facets of functional diversity do not always follow the same pattern. Sometimes, functional richness is not yet affected despite species loss, while functional evenness and divergence are already reducing. Other times, functional richness reduces, while functional evenness and/or divergence increase instead. The contrasting patterns of the three facets of functional diversity show their complementarity among each other and their added value compared to species richness. With increasing climate change, impacts on freshwater communities accelerate, making early mitigation critically important.

Cenozoic colonisation of the Indian Ocean region by the Australian freshwater originating glassperch family Ambassidae (Teleostei)

We examined the phylogeny and biogeography of the glassperch family Ambassidae (Teleostei), which is widely distributed in the freshwater, brackish and marine coastal habitats across the Indo-West Pacific region. We first built a comprehensive time-calibrated phylogeny of Ambassidae using five genes. We then used this tree to reconstruct the evolution of the salinity preference and ancestral areas. Our results indicate that the two largest genera of Ambassidae, Ambassis and Parambassis, are each not monophyletic. The most recent common ancestor of Ambassidae was freshwater adapted and lived in Australia about 56 million years ago. Three independent freshwater-to-marine transitions are inferred, but no marine-to-freshwater ones. To explain the distribution of ambassids, we hypothesise two long-distance marine dispersal events from Australia. A first event was towards Southeast Asia during the early Cenozoic, followed by a second one towards Africa during mid-Cenozoic. The phylogenetic signal associated with the salinity adaptation of these events was not detected, possibly because of the selective extinction of intermediate marine lineages. The Ambassidae shares two characteristics with other freshwater fish groups distributed in continental regions surrounding the Indian Ocean: They are too young to support the hypothesis that their distribution is the result of the fragmentation of Gondwana, but they did not retain the phylogenetic signal of their marine dispersal.

Evolution of the glomerulus in a marine environment and its implications for renal function in terrestrial vertebrates

Nearly a century ago, Homer Smith proposed that the glomerulus evolved to meet the challenge of excretion of water in freshwater vertebrates. This hypothesis has been repeatedly restated in the nephrology and renal physiology literature, even though we now know that vertebrates evolved and diversified in marine (saltwater) environments. A more likely explanation is that the vertebrate glomerulus evolved from the meta-nephridium of marine invertebrates, with the driving force for ultrafiltration being facilitated by the apposition of the filtration barrier to the vasculature (in vertebrates) rather than the coelom (in invertebrates) and the development of a true heart and the more complex vertebrate vascular system. In turn, glomerular filtration aided individual regulation of divalent ions like magnesium, calcium, and sulfate compatible with the function of cardiac and skeletal muscle required for mobile predators. The metabolic cost, imposed by reabsorption of the small amounts of sodium required to drive secretion of these over-abundant divalent ions, was small. This innovation, developed in a salt-water environment, provided a preadaptation for life in freshwater, in which the glomerulus was co-opted to facilitate water excretion, albeit with the additional metabolic demand imposed by the need to reabsorb the majority of filtered sodium. The evolution of the glomerulus in saltwater also provided preadaptation for terrestrial life, where the imperative is conservation of both water and electrolytes. The historical contingencies of this scenario may explain why the mammalian kidney is so metabolically inefficient, with ∼80% of oxygen consumption being used to drive reabsorption of filtered sodium.

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Predator-mediated diversity of stream fish assemblages in a boreal river basin, China

Predator-prey interactions are critical for understanding species composition and community assembly; however, there is still limited research on whether and how the prey species composition or community assembly in natural communities are mediated by predators. To address this question, we performed a field investigation to examine the influence of the presence of Lutra lutra on the diversity of fish communities of the Hunchun River Basin, Jilin Province, China. Our results indicate that L. lutra, as a potential umbrella species and generalist predator in the stream ecosystem, promotes the coexistence of a vast variety of fish taxa, which emphasizes the importance of top-down control in the ecological community. We suggest that L. lutra regulates the fish community assembly likely through the stochastic process. Although this was a pilot study regarding predator-prey interactions, the results highlight the effects of predators on the prey community assembly, and emphasize the role of predators on the maintenance of biodiversity and ecosystem function. Future conservation decisions involving ecosystem biodiversity should require the inclusion of predation intensity. The inclusion of scientific research and protection of umbrella species would thus constitute an additional and important step in biodiversity conservation.

Strong species structure but weak geographical structure in demersal Lake Victoria cichlids

Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably <20,000 years old. Earlier work showed that communities of rocky reef cichlids are composed of many reciprocally monophyletic species despite their very recent origins. Here, we build on this work by studying assemblages of offshore demersal cichlids, adding analyses of within-species spatial structure to the sympatric species structure. We sampled seven multispecies communities along a 6-km-long transect from one side of the Mwanza Gulf to the other side. We investigated whether phenotypically diagnosed putative species are reciprocally monophyletic and whether such monophyly is stable across species geographic ranges. We show that all species are genetically strongly differentiated in sympatry, that they are reciprocally monophyletic, and that monophyly is stable across distribution ranges. We found significant differentiation between geographically distinct populations in two species, but no or weak isolation by distance. We further found subtle but significant morphological differences between all species and a linear relationship between genomic and morphological distance which suggests that differences in morphology begin to accumulate after speciation has already affected genome-wide restrictions of gene flow.

Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes

Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.

Repeated Genetic Targets of Natural Selection Underlying Adaptation of Fishes to Changing Salinity

Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions.

Ecological and Phenotypic Diversification after A Continental Invasion in Neotropical Freshwater Stingrays

Habitat transitions are key potential explanations for why some lineages have diversified and others have not - from Anolis lizards to Darwin's finches. The ecological ramifications of marine-to-freshwater transitions for fishes suggest evolutionary contingency: some lineages maintain their ancestral niches in novel habitats (niche conservatism), whereas others alter their ecological role. However, few studies have considered phenotypic, ecological, and lineage diversification concurrently to explore this issue. Here, we investigated the macroevolutionary history of the taxonomically and ecologically diverse Neotropical freshwater river rays (subfamily Potamotrygoninae), which invaded and diversified in the Amazon and other South American rivers during the late Oligocene to early Miocene. We generated a time-calibrated, multi-gene phylogeny for Potamotrygoninae and reconstructed evolutionary patterns of diet specialization. We measured functional morphological traits relevant for feeding and used comparative phylogenetic methods to examine how feeding morphology diversified over time. Potamotrygonine trophic and phenotypic diversity are evenly partitioned (non-overlapping) among internal clades for most of their history, until 20-16 mya, when more recent diversification suggests increasing overlap among phenotypes. Specialized piscivores (Heliotrygon and Paratrygon) evolved early in the history of freshwater stingrays, while later trophic specialization (molluscivory, insectivory, and crustacivory) evolved in the genus Potamotrygon. Potamotrygonins demonstrate ecological niche lability in diets and feeding apparatus; however, diversification has mostly been a gradual process through time. We suggest that competition is unlikely to have limited the potamotrygonine invasion and diversification in South America.

The origins of global biodiversity on land, sea and freshwater

Many biodiversity studies focus on explaining high tropical species richness, but an equally dramatic yet understudied pattern involves the divergent richness of land, sea and freshwater. Here, we reveal the origins of these richness differences among habitats across animals and plants. Most plant and animal species are terrestrial, although these habitats cover only ~28% of Earth's surface. Marine habitats have fewer species over a larger area (~70%). Freshwater habitats have relatively high richness and exceptional phylogenetic diversity given their tiny area (2%). The relative richness of habitats is related to variation in diversification rates. Based on ancestral reconstructions of habitat, we find that most marine species are descended from marine ancestors and most terrestrial species from freshwater ancestors. Yet, most extant animal richness in freshwater is derived from terrestrial ancestors. Overall, our results reveal the origins of fundamental but neglected biodiversity patterns, and highlight the conservation importance of freshwater habitats.

Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species

Reconstructing past events of hybridization and population size changes are required to understand speciation mechanisms and current patterns of genetic diversity, and ultimately contribute to species' conservation. Sea turtles are ancient species currently facing anthropogenic threats including climate change, fisheries, and illegal hunting. Five of the seven extant sea turtle species are known to currently hybridize, especially along the Brazilian coast where some populations can have ~32%-42% of hybrids. Although frequently observed today, it is not clear what role hybridization plays in the evolutionary diversification of this group of reptiles. In this study, we generated whole genome resequencing data of the five globally distributed sea turtle species to estimate a calibrated phylogeny and the population size dynamics, and to understand the role of hybridization in shaping the genomes of these ancient species. Our results reveal discordant species divergence dates between mitochondrial and nuclear genomes, with a high frequency of conflicting trees throughout the nuclear genome suggesting that some sea turtle species frequently hybridized in the past. The reconstruction of the species' demography showed a general decline in effective population sizes with no signs of recovery, except for the leatherback sea turtle. Furthermore, we discuss the influence of reference bias in our estimates. We show long-lasting ancestral gene flow events within Chelonioidea that continued for millions of years after initial divergence. Speciation with gene flow is a common pattern in marine species, and it raises questions whether current hybridization events should be considered as a part of these species' evolutionary history or a conservation issue.

Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish

Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. However, the genetic architecture underlying these adaptive changes is still poorly understood. Using population genomic approaches, we investigated the genomic architecture that underlies rapid parallel adaptation of Coilia nasus to fresh water by comparing four freshwater-resident populations with their ancestral anadromous population. Linkage disequilibrium network analysis and population genetic analyses revealed two putative large chromosome inversions on LG6 and LG22, which were enriched for outlier loci and exhibited parallel association with freshwater adaptation. Drastic frequency shifts and elevated genetic differentiation were observed for the two chromosome inversions among populations, suggesting that both inversions would undergo divergent selection between anadromous and resident ecotypes. Enrichment analysis of genes within chromosome inversions showed significant enrichment of genes involved in metabolic process, immunoregulation, growth, maturation, osmoregulation, and so forth, which probably underlay differences in morphology, physiology and behavior between the anadromous and freshwater-resident forms. The availability of beneficial standing genetic variation, large optimum shift between marine and freshwater habitats, and high efficiency of selection with large population size could lead to the observed rapid parallel adaptive genomic change. We propose that chromosomal inversions might have played an important role during the evolution of rapid parallel ecological divergence in the face of environmental heterogeneity in C. nasus. Our study provides insights into the genomic basis of rapid adaptation of complex traits in novel habitats and highlights the importance of structural genomic variants in analyses of ecological adaptation.

Comparing diversification rates in lakes, rivers, and the sea

The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.

Locomotor responses to salt stress in native and invasive mud-tidal gastropod populations (Batillaria)

Plasticity in salt tolerance can be crucial for successful biological invasions of novel habitats by marine gastropods. The intertidal snail Batillaria attramentaria, which is native to East Asia but invaded the western shores of North America from Japan 80 years ago, provides an opportunity to examine how environmental salinity may shape behavioral and morphological traits. In this study, we compared the movement distance of four B. attramentaria populations from native (Korea and Japan) and introduced (United States) habitats under various salinity levels (13, 23, 33, and 43 PSU) during 30 days of exposure in the lab. We sequenced a partial mitochondrial CO1 gene to infer phylogenetic relationships among populations and confirmed two divergent mitochondrial lineages constituting our sample sets. Using a statistical model-selection approach, we investigated the effects of geographic distribution and genetic composition on locomotor performance in response to salt stress. Snails exposed to acute low salinity (13 PSU) reduced their locomotion and were unable to perform at their normal level (the moving pace of snails exposed to 33 PSU). We did not detect any meaningful differences in locomotor response to salt stress between the two genetic lineages or between the native snails (Japan vs. Korea populations), but we found significant locomotor differences between the native and introduced groups (Japan or Korea vs. the United States). We suggest that the greater magnitude of tidal salinity fluctuation at the US location may have influenced locomotor responses to salt stress in introduced snails.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.

Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water

Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome-level genome assembly of LMB using PacBio and Hi-C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium-transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high-quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome-level LMB genome will also be a valuable genomic resource for in-depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.

Flatfishes colonised freshwater environments by acquisition of various DHA biosynthetic pathways

The colonisation of freshwater environments by marine fishes has historically been considered a result of adaptation to low osmolality. However, most marine fishes cannot synthesise the physiologically indispensable fatty acid, docosahexaenoic acid (DHA), due to incomplete DHA biosynthetic pathways, which must be adapted to survive in freshwater environments where DHA is poor relative to marine environments. By analysing DHA biosynthetic pathways of one marine and three freshwater-dependent species from the flatfish family Achiridae, we revealed that functions of fatty acid metabolising enzymes have uniquely and independently evolved by multi-functionalisation or neofunctionalisation in each freshwater species, such that every functional combination of the enzymes has converged to generate complete and functional DHA biosynthetic pathways. Our results demonstrate the elaborate patchwork of fatty acid metabolism and the importance of acquiring DHA biosynthetic function in order for fish to cross the nutritional barrier at the mouth of rivers and colonise freshwater environments.

Matsushita et al. demonstrate the evolution of DHA biosynthetic mechanisms in four species of flatfish as some of them colonised freshwater environments. Their analyses show independent changes to the biosynthetic pathways as a way to overcome the lack of exogenous DHA that would typically be available from prey in the marine environment.

Multiple threats imperil freshwater biodiversity in the Anthropocene

Appropriation of fresh water to meet human needs is growing, and competition among users will intensify in a warmer and more crowded world. This essay explains why freshwater ecosystems are global hotspots of biological richness, despite a panoply of interacting threats that jeopardize biodiversity. The combined effects of these threats will soon become detrimental to humans since provision of ecosystem services, such as protein from capture fisheries, can only be sustained if waters remain healthy. Climate change poses an insidious existential threat to freshwater biodiversity in the Anthropocene, but immediate risks from dams, habitat degradation and pollution could well be far greater.

Evolution of epithelial sodium channels: current concepts and hypotheses

The conquest of freshwater and terrestrial habitats was a key event during vertebrate evolution. Occupation of low-salinity and dry environments required significant osmoregulatory adaptations enabling stable ion and water homeostasis. Sodium is one of the most important ions within the extracellular liquid of vertebrates, and molecular machinery for urinary reabsorption of this electrolyte is critical for the maintenance of body osmoregulation. Key ion channels involved in the fine-tuning of sodium homeostasis in tetrapod vertebrates are epithelial sodium channels (ENaCs), which allow the selective influx of sodium ions across the apical membrane of epithelial cells lining the distal nephron or the colon. Furthermore, ENaC-mediated sodium absorption across tetrapod lung epithelia is crucial for the control of liquid volumes lining the pulmonary surfaces. ENaCs are vertebrate-specific members of the degenerin/ENaC family of cation channels; however, there is limited knowledge on the evolution of ENaC within this ion channel family. This review outlines current concepts and hypotheses on ENaC phylogeny and discusses the emergence of regulation-defining sequence motifs in the context of osmoregulatory adaptations during tetrapod terrestrialization. In light of the distinct regulation and expression of ENaC isoforms in tetrapod vertebrates, we discuss the potential significance of ENaC orthologs in osmoregulation of fishes as well as the putative fates of atypical channel isoforms in mammals. We hypothesize that ancestral proton-sensitive ENaC orthologs might have aided the osmoregulatory adaptation to freshwater environments whereas channel regulation by proteases evolved as a molecular adaptation to lung liquid homeostasis in terrestrial tetrapods.

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.

Global determinants of freshwater and marine fish genetic diversity

Genetic diversity is estimated to be declining faster than species diversity under escalating threats, but its spatial distribution remains poorly documented at the global scale. Theory predicts that similar processes should foster congruent spatial patterns of genetic and species diversity, but empirical studies are scarce. Using a mined database of 50,588 georeferenced mitochondrial DNA barcode sequences (COI) for 3,815 marine and 1,611 freshwater fish species respectively, we examined the correlation between genetic diversity and species diversity and their global distributions in relation to climate and geography. Genetic diversity showed a clear spatial organisation, but a weak association with species diversity for both marine and freshwater species. We found a predominantly positive relationship between genetic diversity and sea surface temperature for marine species. Genetic diversity of freshwater species varied primarily across the regional basins and was negatively correlated with average river slope. The detection of genetic diversity patterns suggests that conservation measures should consider mismatching spatial signals across multiple facets of biodiversity.

Biogeographic patterns of genetic diversity are poorly documented, especially for fish species. Here the authors show that (mitochondrial) genetic diversity has global spatial organization patterns with different environmental drivers for marine and freshwater fishes, where genetic diversity is only partly congruent with species richness.

The global decline of freshwater megafauna

Freshwater ecosystems are among the most diverse and dynamic ecosystems on Earth. At the same time, they are among the most threatened ecosystems but remain underrepresented in biodiversity research and conservation efforts. The rate of decline of vertebrate populations is much higher in freshwaters than in terrestrial or marine realms. Freshwater megafauna (i.e., freshwater animals that can reach a body mass ≥30 kg) are intrinsically prone to extinction due to their large body size, complex habitat requirements and slow life-history strategies such as long life span and late maturity. However, population trends and distribution changes of freshwater megafauna, at continental or global scales, remain unclear. In the present study, we compiled population data of 126 freshwater megafauna species globally from the Living Planet Database and available literature, and distribution data of 44 species inhabiting Europe and the United States from literature and databases of the International Union for Conservation of Nature and NatureServe. We quantified changes in population abundance and distribution range of freshwater megafauna species. Globally, freshwater megafauna populations declined by 88% from 1970 to 2012, with the highest declines in the Indomalaya and Palearctic realms (-99% and -97%, respectively). Among taxonomic groups, mega-fishes exhibited the greatest global decline (-94%). In addition, freshwater megafauna experienced major range contractions. For example, distribution ranges of 42% of all freshwater megafauna species in Europe contracted by more than 40% of historical areas. We highlight the various sources of uncertainty in tracking changes in populations and distributions of freshwater megafauna, such as the lack of monitoring data and taxonomic and spatial biases. The detected trends emphasize the critical plight of freshwater megafauna globally and highlight the broader need for concerted, targeted and timely conservation of freshwater biodiversity.

Origins of Afrotropical freshwater fishes

The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.

Evolution: Genomic Signatures of Mimicry and Mimicry of Genomic Signatures

How new species form in the ocean, and thus what determines the diversity of fish in the sea, is not well understood. A study in Caribbean coral-reef fishes sheds light on the genomic underpinnings of diversification in the marine realm.

The joint evolution of the Myxozoa and their alternate hosts: A cnidarian recipe for success and vast biodiversity

The relationships between parasites and their hosts are intimate, dynamic and complex; the evolution of one is inevitably linked to the other. Despite multiple origins of parasitism in the Cnidaria, only parasites belonging to the Myxozoa are characterized by a complex life cycle, alternating between fish and invertebrate hosts, as well as by high species diversity. This inspired us to examine the history of adaptive radiations in myxozoans and their hosts by determining the degree of congruence between their phylogenies and by timing the emergence of myxozoan lineages in relation to their hosts. Recent genomic analyses suggested a common origin of Polypodium hydriforme, a cnidarian parasite of acipenseriform fishes, and the Myxozoa, and proposed fish as original hosts for both sister lineages. We demonstrate that the Myxozoa emerged long before fish populated Earth and that phylogenetic congruence with their invertebrate hosts is evident down to the most basal branches of the tree, indicating bryozoans and annelids as original hosts and challenging previous evolutionary hypotheses. We provide evidence that, following invertebrate invasion, fish hosts were acquired multiple times, leading to parallel cospeciation patterns in all major phylogenetic lineages. We identify the acquisition of vertebrate hosts that facilitate alternative transmission and dispersion strategies as reason for the distinct success of the Myxozoa, and identify massive host specification-linked parasite diversification events. The results of this study transform our understanding of the origins and evolution of parasitism in the most basal metazoan parasites known.

Cerebrovascular β-dystroglycan immunoreactivity in vertebrates: not detected in anurans and in the teleosts Ostariophysi and Euteleostei

The aim of the present paper was to check for the presence of cerebrovascular dystroglycan in vertebrates, because dystroglycan, which is localized in the vascular astroglial end-feet, has a pivotal function in glio-vascular connections. In mammalian brains, the immunoreactivity of β-dystroglycan subunit delineates the vessels. The results of the present study demonstrate similar patterns in other vertebrates, except for anurans and the teleost groups Ostariophysi and Euteleostei. In this study, we investigated 1 or 2 representative species of the main groups of Chondrichthyes, teleost and non-teleost ray-finned fishes, urodeles, anurans, and reptiles. We also investigated 5 mammalian and 3 bird species. Animals were obtained from breeders or fishermen. The presence of β-dystroglycan was investigated immunohistochemically in free-floating sections. Pre-embedding electron microscopical immunohistochemistry on Heterodontus japonicus shark brains demonstrated that in Elasmobranchii, β-dystroglycan is also localized in the perivascular glial end-feet despite the different construction of their blood-brain barrier. The results indicated that the cerebrovascular β-dystroglycan immunoreactivity disappeared separately in anurans, and in teleosts, in the latter group before its division to Ostariophysi and Euteleostei. Immunohistochemistry in muscles and western blots from brain homogenates, however, detected the presence of β-dystroglycan, even in anurans and all teleosts. A possible explanation is that in the glial end-feet, β-dystroglycan is masked in these animals, or disappeared during adaptation to the freshwater habitat.

Netting the Stress Responses in Fish

In the last decade, the concept of animal stress has been stressed thin to accommodate the effects of short-term changes in cell and tissue physiology, major behavioral syndromes in individuals and ecological disturbances in populations. Seyle's definition of stress as "the nonspecific (common) result of any demand upon the body" now encompasses homeostasis in a broader sense, including all the hierarchical levels in a networked biological system. The heterogeneity of stress responses thus varies within individuals, and stressors become multimodal in terms of typology, source and effects, as well as the responses that each individual elicits to cope with the disturbance. In fish, the time course of changes after stress strongly depends on several factors, including the stressful experiences in early life, the vertical transmission of stressful-prone phenotypes, the degree of individual phenotypic plasticity, the robustness and variety of the epigenetic network related to environmentally induced changes, and the intrinsic behavioral responses (individuality/personality) of each individual. The hierarchical heterogeneity of stress responses demands a code that may decrypt and simplify the analysis of both proximate and evolutionary causes of a particular stress phenotype. We propose an analytical framework, the stressotope, defined as an adaptive scenario dominated by common environmental selective pressures that elicit common multilevel acute stress-induced responses and produce a measurable allostatic load in the organism. The stressotope may constitute a blueprint of embedded interactions between stress-related variations in cell states, molecular mediators and systemic networks, a map of circuits that reflect the inherited and acquired stress responses in an ever-changing, microorganismal-loaded medium. Several features of the proposed model are discussed as a starting point to pin down the maximum common stress responses across immune-neuroendocrine relevant physiological levels and scenarios, including the characterization of behavioral responses, in fish.

Emerging threats and persistent conservation challenges for freshwater biodiversity

In the 12 years since Dudgeon et al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e-commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem-level changes through bottom-up and top-down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation-oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.

The nearshore cradle of early vertebrate diversification

Ancestral vertebrate habitats are subject to controversy and obscured by limited, often contradictory paleontological data. We assembled fossil vertebrate occurrence and habitat datasets spanning the middle Paleozoic (480 million to 360 million years ago) and found that early vertebrate clades, both jawed and jawless, originated in restricted, shallow intertidal-subtidal environments. Nearshore divergences gave rise to body plans with different dispersal abilities: Robust fishes shifted shoreward, whereas gracile groups moved seaward. Fresh waters were invaded repeatedly, but movement to deeper waters was contingent upon form and short-lived until the later Devonian. Our results contrast with the onshore-offshore trends, reef-centered diversification, and mid-shelf clustering observed for benthic invertebrates. Nearshore origins for vertebrates may be linked to the demands of their mobility and may have influenced the structure of their early fossil record and diversification.

Explaining the ocean's richest biodiversity hotspot and global patterns of fish diversity

For most marine organisms, species richness peaks in the Central Indo-Pacific region and declines longitudinally, a striking pattern that remains poorly understood. Here, we used phylogenetic approaches to address the causes of richness patterns among global marine regions, comparing the relative importance of colonization time, number of colonization events, and diversification rates (speciation minus extinction). We estimated regional richness using distributional data for almost all percomorph fishes (17 435 species total, including approximately 72% of all marine fishes and approximately 33% of all freshwater fishes). The high diversity of the Central Indo-Pacific was explained by its colonization by many lineages 5.3-34 million years ago. These relatively old colonizations allowed more time for richness to build up through in situ diversification compared to other warm-marine regions. Surprisingly, diversification rates were decoupled from marine richness patterns, with clades in low-richness cold-marine habitats having the highest rates. Unlike marine richness, freshwater diversity was largely derived from a few ancient colonizations, coupled with high diversification rates. Our results are congruent with the geological history of the marine tropics, and thus may apply to many other organisms. Beyond marine biogeography, we add to the growing number of cases where colonization and time-for-speciation explain large-scale richness patterns instead of diversification rates.

Biodiversity and host-parasite cophylogeny of Sphaerospora (sensu stricto) (Cnidaria: Myxozoa)

BACKGROUND

Myxozoa are extremely diverse microscopic parasites belonging to the Cnidaria. Their life-cycles alternate between vertebrate and invertebrate hosts, predominantly in aquatic habitats. Members of the phylogenetically well-defined Sphaerospora (sensu stricto) clade predominantly infect the urinary system of marine and freshwater fishes and amphibians. Sphaerosporids are extraordinary due to their extremely long and unique insertions in the variable regions of their 18S and 28S rDNA genes and due to the formation of motile proliferative stages in the hosts' blood. To date, DNA sequences of only 19 species have been obtained and information on the patterns responsible for their phylogenetic clustering is limited.

METHODS

We screened 549 fish kidney samples from fish of various geographical locations, mainly in central Europe, to investigate sphaerosporid biodiversity microscopically and by 18S rDNA sequences. We performed multiple phylogenetic analyses to explore phylogenetic relationships and evolutionary trends within the Sphaerospora (s.s.) clade, by matching host and habitat features to the resultant 18S rDNA trees. The apparent co-clustering of species from related fish hosts inspired us to further investigate host-parasite co-diversification, using tree-based (CoRE-PA) and distance-based (ParaFit) methods.

RESULTS

Our study considerably increased the number of 18S rDNA sequence data for Sphaerospora (s.s.) by sequencing 17 new taxa. Eight new species are described and one species (Sphaerospora diminuta Li & Desser, 1985) is redescribed, accompanied by sufficient morphological data. Phylogenetic analyses showed that sphaerosporids cluster according to their vertebrate host order and habitat, but not according to geography. Cophylogenetic analyses revealed a significant congruence between the phylogenetic trees of sphaerosporids and of their vertebrate hosts and identified Cypriniformes as a host group of multiple parasite lineages and with high parasite diversity.

CONCLUSIONS

This study significantly contributed to our knowledge of the biodiversity and evolutionary history of the members of the Sphaerospora (s.s.) clade. The presence of two separate phylogenetic lineages likely indicates independent historical host entries, and the remarkable overlap of the larger clade with vertebrate phylogeny suggests important coevolutionary adaptations. Hyperdiversification of sphaerosporids in cypriniform hosts, which have undergone considerable radiations themselves, points to host-driven diversification.

Study of morphological variation of northern Neotropical Ariidae reveals conservatism despite macrohabitat transitions

BACKGROUND

Morphological convergence triggered by trophic adaptations is a common pattern in adaptive radiations. The study of shape variation in an evolutionary context is usually restricted to well-studied fish models. We take advantage of the recently revised systematics of New World Ariidae and investigate skull shape evolution in six genera of northern Neotropical Ariidae. They constitute a lineage that diversified in the marine habitat but repeatedly adapted to freshwater habitats. 3D geometric morphometrics was applied for the first time in catfish skulls and phylogenetically informed statistical analyses were performed to test for the impact of habitat on skull diversification after habitat transition in this lineage.

RESULTS

We found that skull shape is conserved throughout phylogeny. A morphospace analysis revealed that freshwater and marine species occupy extreme ends of the first principal component axis and that they exhibit similar Procrustes variances. Yet freshwater species occupy the smallest shape space compared to marine and brackish species (based on partial disparity), and marine and freshwater species have the largest Procrustes distance to each other. We observed a single case of shape convergence as derived from 'C-metrics', which cannot be explained by the occupation of the same habitat.

CONCLUSIONS

Although Ariidae occupy such a broad spectrum of different habitats from sea to freshwater, the morphospace analysis and analyses of shape and co-variation with habitat in a phylogenetic context shows that conservatism dominates skull shape evolution among ariid genera.

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.

Constructing a 'Chromonome' of Yellowtail (Seriola quinqueradiata) for Comparative Analysis of Chromosomal Rearrangements

To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome. Between yellowtail and Japanese medaka (Oryzias latipes), almost all regions of the chromosomes were conserved and some blocks comprising several markers were translocated. Using the genome information of the spotted gar (Lepisosteus oculatus) as a reference, we further documented syntenic relationships and chromosomal rearrangements that occurred during evolution in four other acanthopterygian species (Japanese medaka, zebrafish, spotted green pufferfish and three-spined stickleback). The evolutionary chromosome translocation frequency was 1.5-2-times higher in yellowtail than in medaka, pufferfish, and stickleback.

Tempo and rates of diversification in the South American cichlid genus Apistogramma (Teleostei: Perciformes: Cichlidae)

Evaluating biodiversity and understanding the processes involved in diversification are noticeable conservation issues in fishes subject to large, sometimes illegal, ornamental trade purposes. Here, the diversity and evolutionary history of the Neotropical dwarf cichlid genus Apistogramma from several South American countries are investigated. Mitochondrial and nuclear markers are used to infer phylogenetic relationships between 31 genetically identified species. The monophyly of Apistogramma is suggested, and Apistogramma species are distributed into four clades, corresponding to three morphological lineages. Divergence times estimated with the Yule process and an uncorrelated lognormal clock dated the Apistogramma origin to the beginning of the Eocene (≈ 50 Myr) suggesting that diversification might be related to marine incursions. Our molecular dating also suggests that the Quaternary glacial cycles coincide with the phases leading to Apistogramma speciation. These past events did not influence diversification rates in the speciose genus Apistogramma, since diversification appeared low and constant through time. Further characterization of processes involved in recent Apistogramma diversity will be necessary.

Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae

Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes.

What Explains Patterns of Diversification and Richness among Animal Phyla?

Animal phyla vary dramatically in species richness (from one species to >1.2 million), but the causes of this variation remain largely unknown. Animals have also evolved striking variation in morphology and ecology, including sessile marine taxa lacking heads, eyes, limbs, and complex organs (e.g., sponges), parasitic worms (e.g., nematodes, platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs that dominate terrestrial ecosystems (arthropods, chordates). Relating this remarkable variation in traits to the diversification and richness of animal phyla is a fundamental yet unresolved problem in biology. Here, we test the impacts of 18 traits (including morphology, ecology, reproduction, and development) on diversification and richness of extant animal phyla. Using phylogenetic multiple regression, the best-fitting model includes five traits that explain ∼74% of the variation in diversification rates (dioecy, parasitism, eyes/photoreceptors, a skeleton, nonmarine habitat). However, a model including just three (skeleton, parasitism, habitat) explains nearly as much variation (∼67%). Diversification rates then largely explain richness patterns. Our results also identify many striking traits that have surprisingly little impact on diversification (e.g., head, limbs, and complex circulatory and digestive systems). Overall, our results reveal the key factors that shape large-scale patterns of diversification and richness across >80% of all extant, described species.

Evolutionary and environmental determinants of freshwater fish thermal tolerance and plasticity

Understanding the extent to which phylogenetic constraints and adaptive evolutionary forces help define the physiological sensitivity of species is critical for anticipating climate-related impacts in aquatic environments. Yet, whether upper thermal tolerance and plasticity are shaped by common evolutionary and environmental mechanisms remains to be tested. Based on a systematic literature review, we investigated this question in 82 freshwater fish species (27 families) representing 829 experiments for which data existed on upper thermal limits and it was possible to estimate plasticity using upper thermal tolerance reaction norms. Our findings indicated that there are strong phylogenetic signals in both thermal tolerances and acclimation capacity, although it is weaker in the latter. We found that upper thermal tolerances are correlated with the temperatures experienced by species across their range, likely because of spatially autocorrelated processes in which closely related species share similar selection pressures and limited dispersal from ancestral environments. No association with species thermal habitat was found for acclimation capacity. Instead, species with the lowest physiological plasticity also displayed the highest thermal tolerances, reflecting to some extent an evolutionary trade-off between these two traits. Although our study demonstrates that macroecological climatic niche features measured from species distributions are likely to provide a good approximation of freshwater fish sensitivity to climate change, disentangling the mechanisms underlying both acute and chronic heat tolerances may help to refine predictions regarding climate change-related range shifts and extinctions.

Cryptic diversity, geographical endemism and allopolyploidy in NE Pacific seaweeds

Background

Molecular markers are revealing a much more diverse and evolutionarily complex picture of marine biodiversity than previously anticipated. Cryptic and/or endemic marine species are continually being found throughout the world oceans, predominantly in inconspicuous tropical groups but also in larger, canopy-forming taxa from well studied temperate regions. Interspecific hybridization has also been found to be prevalent in many marine groups, for instance within dense congeneric assemblages, with introgressive gene-flow being the most common outcome. Here, using a congeneric phylogeographic approach, we investigated two monotypic and geographically complementary sister genera of north-east Pacific intertidal seaweeds (Hesperophycus and Pelvetiopsis), for which preliminary molecular tests revealed unexpected conflicts consistent with unrecognized cryptic diversity and hybridization.

Results

The three recovered mtDNA clades did not match a priori species delimitations. H. californicus was congruent, whereas widespread P. limitata encompassed two additional narrow-endemic species from California - P. arborescens (here genetically confirmed) and P. hybrida sp. nov. The congruence between the genotypic clusters and the mtDNA clades was absolute. Fixed heterozygosity was apparent in a high proportion of loci in P. limitata and P. hybrida, with genetic analyses showing that the latter was composed of both H. californicus and P. arborescens genomes. All four inferred species could be distinguished based on their general morphology.

Conclusions

This study confirmed additional diversity and reticulation within NE Pacific Hesperophycus/Pelvetiopsis, including the validity of the much endangered, modern climatic relict P. arborescens, and the identification of a new, stable allopolyploid species (P. hybrida) with clearly discernable ancestry (♀ H. californicus x ♂ P. arborescens), morphology, and geographical distribution. Allopolyploid speciation is otherwise completely unknown in brown seaweeds, and its unique occurrence within this genus (P. limitata possibly representing a second example) remains enigmatic. The taxonomic separation of Hesperophycus and Pelvetiopsis is not supported and the genera should be synonymized; we retain only the latter. The transitional coastline between Point Conception and Monterey Bay represented a diversity hotspot for the genus and the likely sites of extraordinary evolutionary events of allopolyploid speciation at sympatric range contact zones. This study pinpoints how much diversity (and evolutionary processes) potentially remains undiscovered even on a conspicuous seaweed genus from the well-studied Californian intertidal shores let alone in other, less studied marine groups and regions/depths.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0878-2) contains supplementary material, which is available to authorized users.