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Neotropical mountain streams are important contributors of biological diversity. Two species of the characid genus Rhoadsia differing for an ecologically important morphological trait, body depth, have been described from mountain streams of the western slopes of the Andes in Ecuador. Rhoadsia altipinna is a deeper-bodied species reported from low elevations in southwestern Ecuador and northern Peru, and Rhoadsia minor is a more streamlined species that was described from high elevations (>1200 m) in the Esmeraldas drainage in northwestern Ecuador. Little is known about these species and their validity as distinct species has been questioned. In this study, we examine how their body shape varies along replicated elevational gradients in different drainages of western Ecuador using geometric morphometrics and the fineness ratio. We also use sequences of the mitochondrial cytochrome oxidase c I gene and the second intron of the S7 nuclear gene to examine whether genetic data are consistent with the existence of two species. We found that body depth varies continuously among populations within drainages as a function of elevation, and that body shape overlaps among drainages, such that low elevation populations of R. minor in the Esmeraldas drainage have similar body depths to higher elevation R. altipinna in southern drainages. Although a common general trend of declining body depth with elevation is clear, the pattern and magnitude of body shape divergence differed among drainages. Sequencing of mitochondrial and nuclear genes failed to meet strict criteria for the recognition of two species (e.g., reciprocal monophyly and deep genetic structure). However, there was a large component of genetic variation for the COI gene that segregated among drainages, indicating significant genetic divergence associated with geographic isolation. Continued research on Rhoadsia in western Ecuador may yield significant insight into adaptation and speciation in Neotropical mountain streams.

Cellular immune responses consist of innate and adaptive cell-mediated immune mechanisms, where all leukocyte subpopulations are included. Among these are vital processes such as cell-mediated cytotoxicity and phagocytosis. The main cellular constituents of the fish immune system are macrophages, granulocytes, dendritic cells, NK cells, and cytotoxic T cells. This review provides the latest information on cellular defense mechanisms of fish and provides an overview of the function of the mucosal immune system in maintaining the general health of fish. Here, we discuss the fundamental ideas that underpin mucosal immune responses in teleosts, as well as the innate and adaptive immune cells and the molecules that play a role in these immune responses. Moreover, cytokine molecules and pathways in teleosts have been reported to focus on several kinds of associated immunity. Importantly, we also review antigen processing and presentation. The knowledge reported here will enable better understanding, determination, and modulation of the pathways responsible for protective immunity, thus consequently improving the health of the fish in aquaculture.

Probiotics have been defined as live microorganisms that when administered in adequate amounts confer health benefits to the host. The use of probiotics in aquaculture is an attractive bio-friendly method to decrease the impact of infectious diseases, but is still not an extended practice. Although many studies have investigated the systemic and mucosal immunological effects of probiotics, not all of them have established whether they were actually capable of increasing resistance to different types of pathogens, being this the outmost desired goal. In this sense, in the current paper, we have summarized those experiments in which probiotics were shown to provide increased resistance against bacterial, viral or parasitic pathogens. Additionally, we have reviewed what is known for fish probiotics regarding the mechanisms through which they exert positive effects on pathogen resistance, including direct actions on the pathogen, as well as positive effects on the host.

The luteinizing hormone (LH) and maturation-inducing steroids (MIS), such as 17α,20β-dihydroxy-4-pregnen-3-one, regulate the final oocyte maturation in teleosts. Oocyte maturational competence (OMC) and ovulatory competence measure the sensitivity to MIS for oocyte maturation and ovulation, respectively. However, the molecular mechanisms underlying the acquisition of ovulatory competence remain unknown. Sturgeons are an excellent research model for investigating these mechanisms. We examined the seasonal profiles of OMC and ovulatory competence in vitro and the expression of 17 ovulation-related gene candidates using quantitative PCR in Amur sturgeon ovarian follicles. The ovulatory competence was induced by the LH-releasing hormone analog (LHRHa) priming injection after acquiring the OMC, which was spontaneously induced in spring or autumn. Seven genes, including the tissue-type plasminogen activator (plat), were enhanced following the LHRHa priming injection in ovarian follicles sampled from anovulated and ovulated fish. The activin receptor type 1 (acvr1) and prostaglandin G/H synthase 2 (ptgs2) were only upregulated in ovulated fish. Our results suggest that plat/plasmin and prostaglandin (PG)/PG receptor systems are essential for sturgeon ovulation, similar to other vertebrates. Notably, successful ovulation depends on a sufficient PG synthesis, and mediators activating the PG/PG receptor system are essential for acquiring the ovulatory competence. We provide the first report of ovulation-related gene alterations in the ovarian follicles of Amur sturgeons.

As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.

Climate change is increasing global temperatures and intensifying the frequency and severity of extreme heat waves. How organisms will cope with these changes depends on their inherent thermal tolerance, acclimation capacity, and ability for evolutionary adaptation. Yet, the potential for adaptation of upper thermal tolerance in vertebrates is largely unknown. We artificially selected offspring from wild-caught zebrafish (Danio rerio) to increase (Up-selected) or decrease (Down-selected) upper thermal tolerance over six generations. Selection to increase upper thermal tolerance was also performed on warm-acclimated fish to test whether plasticity in the form of inducible warm tolerance also evolved. Upper thermal tolerance responded to selection in the predicted directions. However, compared to the control lines, the response was stronger in the Down-selected than in the Up-selected lines in which evolution toward higher upper thermal tolerance was slow (0.04 ± 0.008 °C per generation). Furthermore, the scope for plasticity resulting from warm acclimation decreased in the Up-selected lines. These results suggest the existence of a hard limit in upper thermal tolerance. Considering the rate at which global temperatures are increasing, the observed rates of adaptation and the possible hard limit in upper thermal tolerance suggest a low potential for evolutionary rescue in tropical fish living at the edge of their thermal limits.

With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.

Understanding how marine organisms will be affected by global change is of primary importance to ensure ecosystem functioning and nature contributions to people. This study meets the call for addressing how life-history traits mediate effects of ocean acidification on fish. We built a database of overall and trait-mediated responses of teleost fish to future CO₂ levels by searching the scientific literature. Using a meta-analytical approach, we investigated the effects of projected CO₂ levels by IPCC for 2050–2070 and 2100 on fish eco-physiology and behavior from 320 contrasts on 42 species, stemming from polar to tropical regions. Moreover, since organisms may experience a mosaic of carbonate chemistry in coastal environments (e.g., in estuaries, upwelling zones and intertidal habitats), which may have higher 𝑝CO₂ values than open ocean waters, we assessed responses from additional 103 contrasts on 21 fish species using 𝑝CO₂ levels well above IPCC projections. Under mid-century and end-of-century CO₂ emission scenarios, we found multiple CO₂-dose-dependent effects on calcification, resting metabolic rate, yolk, and behavioral performances, along with increased predation risk and decreased foraging, particularly for larvae. Importantly, many of the traits considered will not confer fish tolerance to elevated CO₂ and far-reaching ecological consequences on fish population replenishment and community structure will likely occur. Extreme CO₂ levels well above IPCC projections showed effects on fish mortality and calcification, while growth, metabolism, and yolk were unaffected. CO₂ exposures in short-term experiments increased fish mortality, which in turn decreased in longer-term exposures. Whatever the elevated CO₂ levels considered, some key biological processes (e.g., reproduction, development, habitat choice) were critically understudied. Fish are an important resource for livelihoods in coastal communities and a key component for stability of marine ecosystems. Given the multiple trait-mediated effects evidenced here, we stress the need to fill the knowledge gap on important eco-physiological processes and to expand the number and duration of ocean acidification studies to multi-generational, multiple stressor (e.g., warming, hypoxia, fishing), and species interactions experiments to better elucidate complex ecosystem-level changes and how these changes might alter provisioning of ecosystem services.

The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multispecies coalescent (MSC) model, we here develop a new method combining the single-nucleotide polymorphism-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the MSC model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new restriction-site associated DNA-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.

CD4 is a nonpolymorphic transmembrane glycoprotein molecule that is expressed on the surface of T-helper cells and plays an essential role in the immune response. It functions as a coreceptor with the T-cell receptor by binding to major histocompatibility complex class II on the surface of dendritic cells that present antigens. CD4 + T cells hold a key position in coordinating the immune system through production of several cytokines after activation and differentiation. The CD4 + T helper subtypes (T-helper 1, T-helper 2, T-helper 17, T-helper 9, and regulatory-T cells) perform different immune functions subsequent to their differentiation from the naive T cells. Different types of CD4 + T cells require different cytokines such as drivers and effectors, as well as master transcription factors for their activation. Fish cells that express CD4-related genes are activated in the presence of a pathogen and release cytokines against the pathogen. This review highlights the types of CD4 + T cells in fish and describes their direct role in cell-mediated and humoral immunity for protection against the intracellular bacterial as well as viral infections in fish.