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Radical environmental change that provokes population decline can impose constraints on the sources of genetic variation that may enable evolutionary rescue. Adaptive toxicant resistance has rapidly evolved in Gulf killifish (Fundulus grandis) that occupy polluted habitats. We show that resistance scales with pollution level and negatively correlates with inducibility of aryl hydrocarbon receptor (AHR) signaling. Loci with the strongest signatures of recent selection harbor genes regulating AHR signaling. Two of these loci introgressed recently (18 to 34 generations ago) from Atlantic killifish (F. heteroclitus). One introgressed locus contains a deletion in AHR that confers a large adaptive advantage [selection coefficient (s) = 0.8]. Given the limited migration of killifish, recent adaptive introgression was likely mediated by human-assisted transport. We suggest that interspecies connectivity may be an important source of adaptive variation during extreme environmental change.

Marsh-resident fishes play important roles as both predators and prey in coastal systems, influence secondary production, and are important trophic links to adjacent coastal waters. As such, they also serve as sentinel species in efforts to understand the magnitude and implications of anthropogenic habitat disturbance or degradation. An evaluation of the juvenile and adult marsh fish response to the Macondo oil spill in 2010 was conducted in 2012 and 2013 by sampling in both oiled and unoiled marshes in coastal Louisiana. To complement this analysis, we also examined marsh-fish assemblage structure across several subhabitats (marsh edge, creeks, ponds, depressions). The fauna, collected with traps, was dominated by cyprinodontiform fishes (Fundulus grandis, Fundulus xenicus) and complemented by others in this group (Cyprinodon variegatus, Poecilia latipinna, Fundulus pulvereus, Fundulus jenkinsi, Fundulus similis). Among the dominant species, abundance was often the highest in ponds and marsh surface depressions, with many fish species also commonly found in creeks, but few fish were collected along the marsh edge. Comparisons across representative oiled and unoiled sites from Caminada, Terrebonne, and Barataria Bays did not reflect any consistent differences in species composition, abundance, and size as a function of oiling 2–3 years after the oil spill reached Louisiana marshes. This interpretation may be confounded by multiple stressors, including natural events (e.g., oil redistribution by storms, and seasonal flooding of the marsh surface), and other man-made perturbations (e.g., freshwater discharge).

Freshwater invasions have occurred worldwide with significant ecological, evolutionary, and economic impacts on recipient ecosystems. Researchers now have access to a combination of approaches to better identify their potential ecological impacts on recipient communities. We used an integrative approach based on morphological traits, stomach contents, and stable isotope ratios (δ13C and δ15N) to examine multiple dimensions of the niche of native Texas cyprinodontids, Red River pupfish (Cyprinodon rubrofluviatilis) and plains killifish (Fundulus zebrinus), and their sympatric invasive congeners sheepshead minnow (C. variegates) and gulf killifish (F. grandis). We analyzed specimens from the Brazos River and Red River basins in Texas collected during multiple surveys. Because of their phylogenetic relatedness, we predicted high overlap in the feeding habits and habitat-use between native and invasive congeners. A principal component analysis performed on 24 morphological traits associated with habitat-use and feeding ecology suggested some overlap on trait space occupied by the two Cyprinodon species, but no overlap between the two Fundulus species. High overlap on dietary and isotopic niche space was observed between the native and invasive Cyprinodon congeners. There was a large degree of seasonal variation in all four species stomach contents and isotopic signatures, which could be partially explained by low sampling sizes across certain seasons. While species differed in their trait space, similarities in the feeding ecology between cyprinodontid congeners could lead to negative ecological interactions related to food resources depending on the time of year. Our findings highlight the needs for continued monitoring of invasive cyprinodontids to prevent their spread into upstream reaches of the Brazos River to ensure conservation of native congeners.

Abstract Addition of canals and levees to wetlands is common in hydrological management. Permanently flooded canals provide fishes with refuge from desiccation and corridors for long-distance movement, but also may present high risk of predation. Levees create barriers to movement. We evaluated the effect of canals and levees on the movement of fish in seasonally fluctuating marshes in Everglades National Park between 2003 and 2016. We used directional traps to quantify activity and directional movement of seven species of fishes moving through marshes near canals and levees, and farther into the wetland. Eastern mosquitofish (Gambusia holbrooki) were ubiquitous, were active at all sites throughout the year, and moved towards canals consistent with their use as refuge habitat. Sailfin mollies (Poecilia latipinna) and bluefin killifish (Lucania goodei) were also likely to swim towards canals as water levels dropped in the dry season. Flagfish (Jordanella floridae), golden topminnows (Fundulus chrysotus), and marsh killifish (F. confluentus) used wetlands associated with anthropogenic structures but showed no directional bias with respect to canals and these species did not appear to use them as a drought refuge. Non-native African Jewelfish (Hemichromis letourneauxi) displayed directed movement related to canals, but were most active at sites distant from canals. This study provides evidence for interspecific differences among seven fishes in how they move through a marsh near different anthropogenic structures and in different seasons of the hydrologic year. Modification of wetland landscapes with structures has implications for species sorting and metacommunity dynamics filtered by species-specific behavioral traits. Monitoring efforts like this support understanding how important members of the community, like small fishes, respond to environmental and anthropogenic factors that are subject to management decisions.

We used massively parallel sequencing (pyrosequencing) of 16S rRNA genes to compare the composition of microbial communities in the guts of 12 bony fish and 3 shark species. The species analyzed encompass herbivores and carnivores with varied digestive physiologies, are classified as pelagic and demersal species, and reside in estuarine to marine environments. We also compared the gut microbial assemblages of wild and cultured Fundulus heteroclitus and of juvenile and adult Lagodon rhomboides. A total of 1 214 355 sequences were filtered, denoised, trimmed, and then sorted into operational taxonomic units (OTUs) based on 97% sequence similarity. Bacteria representing 17 phyla were found among the sampled fish, with most fish hosting between 7 and 15 phyla. Proteobacteria OTUs were present in all fish and often dominated the libraries (3.0 to 98%; average: 61%). Firmicutes were also prevalent, but at a lower relative abundance, ranging between 1.3 and 45% (average: 17%). In most cases, the gut microflora of individual fish of a given species contained many of the same OTUs; however, some species (e.g. great barracuda) shared few OTUs among the individuals sampled. Although no single OTU was shared among all fish species, many of the OTUs present in one species’ core group were also found in the core groups of other species. Several OTUs were consistently found in the guts of multiple species, suggesting that these OTUs may be important contributors to fish gut functions such as digestion, nutrient absorption, and immune response.

Hybridization and introgression appear more common in rapidly evolving groups, suggesting an important role in the evolutionary process. Detailed studies of how extrinsic or intrinsic forces regulate hybridization and introgression have the potential for broadening our understanding of mechanisms generating diversity. Species in the Fundulus notatus species complex have broad overlapping ranges and occur in replicated hybrid zones along predictable stream gradients. Typical hybrid zone structure has Fundulus olivaceus in headwaters, F. notatus downstream, and hybrid zones near confluences or abrupt shifts in habitat. Rarely, the typical upstream-downstream orientation is reversed raising questions as to how hybrid zones are formed and maintained. We used next-generation sequencing data to study hybridization and introgression in hybrid zones in neighboring drainages that differ in orientation (typical and reversed). We predicted extrinsic forces linked to stream gradients would result in noticeable differences between the two. Contrary to predictions, the data indicate the hybrid zones are remarkably similar. We used individual-based simulations to explore the potential role of intrinsic and extrinsic forces in generating and maintaining typical and reversed hybrid zones. Simulation results were consistent with reversed hybrid zones being formed from stochastic processes combined with strong intrinsic forces and weak extrinsic forces.

Stable isotopes of carbon, nitrogen, and sulfur are used as ecological tracers for a variety of applications, such as studies of animal migrations, energy sources, and food web pathways. Yet uncertainty relating to the time period integrated by isotopic measurement of animal tissues can confound the interpretation of isotopic data. There have been a large number of experimental isotopic diet shift studies aimed at quantifying animal tissue isotopic turnover rate λ (%·day(-1), often expressed as isotopic half-life, ln(2)/λ, days). Yet no studies have evaluated or summarized the many individual half-life estimates in an effort to both seek broad-scale patterns and characterize the degree of variability. Here, we collect previously published half-life estimates, examine how half-life is related to body size, and test for tissue- and taxa-varying allometric relationships. Half-life generally increases with animal body mass, and is longer in muscle and blood compared to plasma and internal organs. Half-life was longest in ecotherms, followed by mammals, and finally birds. For ectotherms, different taxa-tissue combinations had similar allometric slopes that generally matched predictions of metabolic theory. Half-life for ectotherms can be approximated as: ln (half-life) = 0.22*ln (body mass) + group-specific intercept; n = 261, p<0.0001, r2 = 0.63. For endothermic groups, relationships with body mass were weak and model slopes and intercepts were heterogeneous. While isotopic half-life can be approximated using simple allometric relationships for some taxa and tissue types, there is also a high degree of unexplained variation in our models. Our study highlights several strong and general patterns, though accurate prediction of isotopic half-life from readily available variables such as animal body mass remains elusive.

Variation among populations in gene expression should be related to the accumulation of random-neutral changes and evolution by natural selection. The following evolutionary analysis has general applicability to biological and medical science because it accounts for genetic relatedness and identifies patterns of expression variation that are affected by natural selection. To identify genes evolving by natural selection, we allocate the maximum amongpopulation variation to genetic distance and then examine the remaining variation relative to a hypothesized important ecological parameter (temperature). These analyses measure the expression of metabolic genes in common-gardened populations of the fish Fundulus heteroclitus whose habitat is distributed along a steep thermal gradient. Although much of the variation in gene expression fits a null model of neutral drift, the variation in expression for 22% of the genes that regress with habitat temperature was far greater than could be accounted for by genetic distance alone. The most parsimonious explanation for amongpopulation variation for these genes is evolution by natural selection. In addition, many metabolic genes have patterns of variation incongruent with neutral evolution: They have too much or too little variation. These patterns of biological variation in expression may reflect important physiological or ecological functions.

Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access. We conducted mesocosm experiments using a fish, a crustacean, and two scyphomedusae to investigate how environmental DNA (eDNA) shedding differs between animal forms and how long eDNA can persist in waters of different temperature and light conditions. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest eDNA shedding rate and that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. These findings fill critical knowledge gaps regarding variation in shedding and decay of eDNA across different animal forms under a range of realistic marine temperature and light conditions.

We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4-5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms.