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Ancient, species-poor lineages persistently occur across the Tree of life. These lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils. Halecomorphi is a lineage of ray-finned fishes that diverged from its closest relatives before 200 Ma and is represented by only one living species in eastern North America, the bowfin, Amia calva Linnaeus. Here, we use double digest restriction-site-associated DNA sequencing and morphology to illuminate recent speciation in bowfins. Our results support the delimitation of a second living species of Amia , with the timing of diversification dating to the Plio-Pleistocene. This delimitation expands the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development, yet is facing growing conservation threats driven by the caviar fishery.

SummaryAncient, species-poor lineages persistently occur across the Tree of Life. These evolutionarily unique lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils [1, 2]. Halecomorphi is a major clade of ray-finned fishes that diverged from its closest relatives over 200 million years ago [3, 4] yet is represented by only one recognized living species in eastern North America, the Bowfin Amia calva Linnaeus. Here, we use double digest restriction-site associated DNA (ddRAD) sequencing and high-resolution computed tomography to illuminate recent speciation in the bowfins. Our results support the resurrection of a second living species of Bowfin with the timing of diversification dating to the Pleistocene. In turn, we expand the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development [2, 3, 5], yet is facing growing conservation threats driven by the caviar fishery [6].

The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era., Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.

Production and outmigration of young-of-year (YOY) northern pike from natal sites in Lower Green Bay, WI, USA, were documented over three consecutive years (2013-2015). We tested the hypothesis that spawning success and outmigration characteristics of YOY northern pike would vary among natural and anthropogenically modified habitats. Sixteen focal study locations were surveyed, including a restored natural wetland, agricultural drainage ditches, a flooded forested wetland and several unimpounded tributaries. We collected 1469 YOY northern pike with most individuals (N = 1163) originating from a flooded forested wetland on the east shore. Most sites produced YOY in all years (range N = 2-1145 individuals among study years). Outmigration ranged between 1 and 40 days during 2013-2015. Greater production and extended outmigration times occurred at most sites in 2014 (range 17-40 days) when the region experienced a late spring with heavy precipitation. In contrast, the lowest production and shortest outmigration period occurred at most sites in 2015 (range 14-23 days) when environmental conditions reflected regional averages. Outmigration began nearly 3 weeks earlier in 2015 (5/8) than in other study years (8 June 2013 and 25 May 2014). Total length (TL) of outmigrating northern pike ranged between 17 and 138 mm. Total length of YOY was significantly different among sites in 2013 and 2014, with the smallest fish (17 mm TL) outmigrating from agricultural ditches in both years. There were no significant variations in size among sites in 2015 (range 21-95 mm TL). Our results indicate significant variation in YOY northern pike outmigration characteristics within Lower Green Bay that may reflect the interplay between adult spawning site selection and annual weather patterns. Our findings highlight the importance of quantifying overlooked habitats in regions of mixed development.

The bowfin fish (Amia calva) diverged before the genome duplication in teleost fishes, and its archetypical body plan and slow rate of molecular evolution make it a key species for genomic exploration as a basal representative of the neopterygian fishes. To investigate the evolution and development of ray-finned fishes, we generated a chromosome-level genome assembly for bowfin that enables gene-order analyses which settle its long-debated, phylogenetic relationship with gars. We analyze the genomic underpinnings of the bowfin’s unique combination of derived and ancestral phenotypes involving the immune system as well as scale, respiratory organ, and skeletal development. By detailing chromatin accessibility and gene expression through bowfin development, we connect developmental gene regulatory loci across vertebrates. We illustrate the utility of these genomic resources to connect developmental evolution across bony fishes, showing the importance of bowfin in understanding vertebrate biology and diversity.

Modern zoos and aquariums aspire to contribute significantly to biodiversity conservation and research. For example, conservation research is a key accreditation criterion of the Association of Zoos and Aquariums (AZA). However, no studies to date have quantified this contribution. We assessed the research productivity of 228 AZA members using scientific publications indexed in the ISI Web of Science (WoS) database between 1993 and 2013 (inclusive). AZA members published 5175 peer-reviewed manuscripts over this period, with publication output increasing over time. Most publications were in the zoology and veterinary science subject areas, and articles classified as “biodiversity conservation” by WoS averaged 7% of total publications annually. From regression analyses, AZA organizations with larger financial assets generally published more, but research-affiliated mission statements were also associated with increased publication output. A strong publication record indicates expertise and expands scientific knowledge, enhancing organizational credibility. Institutions aspiring for higher research productivity likely require a dedicated research focus and adequate institutional support through research funding and staffing. We recommend future work build on our results by exploring links between zoo and aquarium research productivity and conservation outcomes or uptake.

The spotted gar (Lepisosteus oculatus) shows a disjunct natural distribution, with a core population extending from the central Mississippi River Basin to the U.S. gulf coast and a peripheral population in the southern Great Lakes Basin. Despite significant conservation concerns for this species in the Great Lakes watersheds where it occurs, few genetic examinations and comparisons of these populations have been performed. We investigated inter- and intrapopulational variation in several mitochondrial genetic markers (cytochrome oxidase subunit I, COI; cytochrome oxidase subunit II, COII; and 16S rRNA, 16S) from spotted gars taken from core and peripheral populations. Genetic diversity was highest in the Mississippi River Basin and lowest in the Great Lakes Basin, while the Nueces River Basin (Texas) population showed the greatest level of divergence from other populations. Average genetic distance among core and peripheral populations was over an order of magnitude less than that seen between L. oculatus and its sister species, the Florida gar (L. platyrhincus), although a significant correlation was found between genetic and geographical distance in L. oculatus. Genetic divergence in spotted gars is likely to be related to a combination of geographic isolation and founder effects associated with recent colonization following glacial retreat. Despite its apparent lack of significant genetic differentiation or haplotype diversity, the Great Lakes population of spotted gars has previously been shown to be a unique component of the species, and additional studies are needed to determine the genetic mechanisms underlying regional adaptations as well as potential morphological differentiation among spotted gar populations.

Peripheral populations occupy the edge of a species' range and may exhibit adaptations to potentially “harsher” marginal environments compared with core populations. The peripheral population of Spotted Gar Lepisosteus oculatus in the Great Lakes basin represents the northern edge of the species' range and is completely disjunct from the core Mississippi River basin population. Age-0 Spotted Gars from the peripheral population experience a growing season approximately half that of the core population but reach similar sizes by winter, suggesting potential for countergradient variation in growth, i.e. an evolutionary response to an environmental gradient such as latitude to compensate for the usual phenotypic effect of that gradient. In this study we used two common garden experiments to investigate potential countergradient variation in growth of young-of-year Spotted Gars from peripheral populations in comparison with those from core populations. Our first experiment showed that in a common envir...

Gars (family Lepisosteidae) serve important roles as apex predators in freshwater ecosystems., helping to balance fish populations. Several gar species are exploited as food and game fish, and some species are classified as vulnerable due to habitat loss. New molecular techniques to detect, monitor, and identify environmental DNA from gars might help inform management and conservation efforts for these interesting fish. Therefore the goal of this project was to develop and test PCR primers for gars, using specimens of all seven gar species, which are on exhibit at the Belle Isle Aquarium in Detroit, Michigan. Focusing on the mitochondrial gene for cytochrome oxidase I (COI), we first designed primers to amplify DNA from all species of gars (“universal gar primers”) and confirmed their specificity in silico. These primers amplified DNA from all seven species, and species identities were confirmed by sequencing the PCR products. Only one of three ostensible Shortnose Gar Lepisosteus platostomus spec...

Recreational angling for gars Lepisosteidae has become more popular in recent years; however, the fundamental understanding of population dynamics needed for effective management and conservation is lacking. Age data are essential for describing population dynamic rate functions, but few studies have addressed selection of ideal calcified structures for use in estimating ages in gars. We collected Spotted Gars Lepisosteus oculatus, Shortnose Gars L. platostomus, and Longnose Gars L. osseus from twelve Illinois waterbodies to assess the relative bias and precision of age estimates among branchiostegal rays, pectoral fin rays, cleithra, and sagittal otoliths. Age assignments differed among calcified structures for all three species. Branchiostegal rays underestimated the age of young fish and overestimated the age of old fish relative to all other structures. Pectoral fin rays consistently underestimated age relative to other structures and produced the lowest mean and maximum age estimates. Low rel...

We evaluated the performance of the Wisconsin bioenergetics model for lake trout Salvelinus namaycush that were fed ad libitum in laboratory tanks under regimes of low activity and high activity. In addition, we compared model performance under two different model algorithms: (1) balancing the lake trout energy budget on day t based on lake trout energy density on day t and (2) balancing the lake trout energy budget on day t based on lake trout energy density on day t + 1. Results indicated that the model significantly underestimated consumption for both inactive and active lake trout when algorithm 1 was used and that the degree of underestimation was similar for the two activity levels. In contrast, model performance substantially improved when using algorithm 2, as no detectable bias was found in model predictions of consumption for inactive fish and only a slight degree of overestimation was detected for active fish. The energy budget was accurately balanced by using algorithm 2 but not by us...

Extant gars represent the remaining members of a formerly diverse assemblage of ancient ray-finned fishes and have been the subject of multiple phylogenetic analyses using morphological data. Here, we present the first hypothesis of phylogenetic relationships among living gar species based on molecular data, through the examination of gene tree heterogeneity and coalescent species tree analyses of a portion of one mitochondrial (COI) and seven nuclear (ENC1, myh6, plagl2, S7 ribosomal protein intron 1, sreb2, tbr1, and zic1) genes. Individual gene trees displayed varying degrees of resolution with regards to species-level relationships, and the gene trees inferred from COI and the S7 intron were the only two that were completely resolved. Coalescent species tree analyses of nuclear genes resulted in a well-resolved and strongly supported phylogenetic tree of living gar species, for which Bayesian posterior node support was further improved by the inclusion of the mitochondrial gene. Species-level relationships among gars inferred from our molecular data set were highly congruent with previously published morphological phylogenies, with the exception of the placement of two species, Lepisosteus osseus and L. platostomus. Re-examination of the character coding used by previous authors provided partial resolution of this topological discordance, resulting in broad concordance in the phylogenies inferred from individual genes, the coalescent species tree analysis, and morphology. The completely resolved phylogeny inferred from the molecular data set with strong Bayesian posterior support at all nodes provided insights into the potential for introgressive hybridization and patterns of allopatric speciation in the evolutionary history of living gars, as well as a solid foundation for future examinations of functional diversification and evolutionary stasis in a "living fossil" lineage.

Based on a laboratory experiment, we estimated the net trophic transfer efficiency of methylmercury to lake trout Salvelinus namaycush from its prey to be equal to 76.6 %. Under the assumption that gross trophic transfer efficiency of methylmercury to lake trout from its prey was equal to 80 %, we estimated that the rate at which lake trout eliminated methylmercury was 0.000244 day(-1). Our laboratory estimate of methylmercury elimination rate was 5.5 times lower than the value predicted by a published regression equation developed from estimates of methylmercury elimination rates for fish available from the literature. Thus, our results, in conjunction with other recent findings, suggested that methylmercury elimination rates for fish have been overestimated in previous studies. In addition, based on our laboratory experiment, we estimated that the net trophic transfer efficiency of inorganic mercury to lake trout from its prey was 63.5 %. The lower net trophic transfer efficiency for inorganic mercury compared with that for methylmercury was partly attributable to the greater elimination rate for inorganic mercury. We also found that the efficiency with which lake trout retained either methylmercury or inorganic mercury from their food did not appear to be significantly affected by the degree of their swimming activity.

Population fecundity can vary through time, sometimes owing to changes in adult condition. Consideration of these fecundity changes can improve understanding of recruitment variation. Herein, we estimated fecundity of Lake Michigan bloater Coregonus hoyi during December 2005 and February 2006. Bloater recruitment has been highly variable from 1962 to present, and consistently poor since 1992. We compared our fecundity vs. weight regression to a previously published regression that used fish sampled in October 1969. We wanted to develop a new regression for two reasons. First, it should be more accurate because it uses fish collected closer to spawning, thus minimizing the potential for atresia (egg reabsorption) which could bias fecundity high. Second, we hypothesized that fecundity would be lower in 2006 because adult condition was 41% lower in 2006 compared to 1969, likely owing to the decline of Diporeia spp, a primary prey for bloater. Although the slope of the fecundity versus weight regression was similar between the years, fecundity was 24% lower in 2006 than in 1969 for bloater weighing between 70 and 240 g. Whether this was the result of the difference in sampling time prior to spawning or of differences in condition is unknown. We also found no relationship between maternal size and mature oocyte size. Incorporating our updated fecundity regression into a stock/recruit model failed to improve the model fit, indicating that the low bloater recruitment that has been observed since the early 1990s is not solely the result of reduced fecundity.

In this paper, hierarchical Bayesian methods for the analysis of crossover designs are developed. First, we consider two hierarchical prior structures yielding posterior quantities that can be obtained via numerical integration. We illustrate this method with an analysis of two well-known data sets. Then we consider more flexible prior structures and a corresponding Markov chain Monte Carlo analysis of the resulting posterior distribution. We illustrate this method using data from a study conducted at Eli Lilly and Company. Throughout, we concentrate on inferences involving the carryover effect.

A technique for laboratory estimation of net trophic transfer efficiency (γ) of polychlorinated biphenyl (PCB) congeners to piscivorous fish from their prey is described herein. During a 135-day laboratory experiment, we fed bloater (Coregonus hoyi) that had been caught in Lake Michigan to lake trout (Salvelinus namaycush) kept in eight laboratory tanks. Bloater is a natural prey for lake trout. In four of the tanks, a relatively high flow rate was used to ensure relatively high activity by the lake trout, whereas a low flow rate was used in the other four tanks, allowing for low lake trout activity. On a tank-by-tank basis, the amount of food eaten by the lake trout on each day of the experiment was recorded. Each lake trout was weighed at the start and end of the experiment. Four to nine lake trout from each of the eight tanks were sacrificed at the start of the experiment, and all 10 lake trout remaining in each of the tanks were euthanized at the end of the experiment. We determined concentrations of 75 PCB congeners in the lake trout at the start of the experiment, in the lake trout at the end of the experiment, and in bloaters fed to the lake trout during the experiment. Based on these measurements, γ was calculated for each of 75 PCB congeners in each of the eight tanks. Mean γ was calculated for each of the 75 PCB congeners for both active and inactive lake trout. Because the experiment was replicated in eight tanks, the standard error about mean γ could be estimated. Results from this type of experiment are useful in risk assessment models to predict future risk to humans and wildlife eating contaminated fish under various scenarios of environmental contamination.

We performed two controlled experiments to determine the amount of mass-dependent and mass-independent fractionation (MDF and MIF) of methylmercury (MeHg) during trophic transfer into fish. In experiment 1, juvenile yellow perch (Perca flavescens) were raised in captivity on commercial food pellets and then their diet was either maintained on unamended food pellets (0.1 μg/g MeHg) or was switched to food pellets with 1.0 μg/g or 4.0 μg/g of added MeHg, for a period of 2 months. The difference in δ(202)Hg (MDF) and Δ(199)Hg (MIF) between fish tissues and food pellets with added MeHg was within the analytical uncertainty (δ(202)Hg, 0.07 ‰; Δ(199)Hg, 0.06 ‰), indicating no isotope fractionation. In experiment 2, lake trout (Salvelinus namaycush) were raised in captivity on food pellets and then shifted to a diet of bloater (Coregonus hoyi) for 6 months. The δ(202)Hg and Δ(199)Hg of the lake trout equaled the isotopic composition of the bloater after 6 months, reflecting reequilibration of the Hg isotopic composition of the fish to new food sources and a lack of isotope fractionation during trophic transfer. We suggest that the stable Hg isotope ratios in fish can be used to trace environmental sources of Hg in aquatic ecosystems.

Lake trout (Salvelinus namaycush) were fed bloater (Coregonus hoyi) in eight laboratory tanks over a 135-d experiment. At the start of the experiment, four to nine fish in each tank were sacrificed, and the concentrations of 75 polychlorinated biphenyl (PCB) congeners within these fish were determined. Polychlorinated biphenyl congener concentrations were also determined in the 10 lake trout remaining in each of the eight tanks at the end of the experiment as well as in the bloater fed to the lake trout. Each lake trout was weighed at the start and the end of the experiment, and the amount of food eaten by the lake trout was recorded. Using these measurements, net trophic transfer efficiency (γ) from the bloater to the lake trout in each of the eight tanks was calculated for each of the 75 congeners. Results showed that γ did not vary significantly with the degree of chlorination of the PCB congeners, and γ averaged 0.66 across all congeners. However, γ did show a slight, but significant, decrease as log K(OW) increased from 6.0 to 8.2. Activity level of the lake trout did not have a significant effect on γ.