Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

You Better Repeat It: Complex CO2 × Temperature Effects in Atlantic Silverside Offspring Revealed by Serial Experimentation

Concurrent ocean warming and acidification demand experimental approaches that assess biological sensitivities to combined effects of these potential stressors. Here, we summarize five CO2 × temperature experiments on wild Atlantic silverside, Menidia menidia, offspring that were reared under factorial combinations of CO2 (nominal: 400, 2200, 4000, and 6000 µatm) and temperature (17, 20, 24, and 28 °C) to quantify the temperature-dependence of CO2 effects in early life growth and survival. Across experiments and temperature treatments, we found few significant CO2 effects on response traits. Survival effects were limited to a single experiment, where elevated CO2 exposure reduced embryo survival at 17 and 24 °C. Hatch length displayed CO2 × temperature interactions due largely to reduced hatch size at 24 °C in one experiment but increased length at 28 °C in another. We found no overall influence of CO2 on larval growth or survival to 9, 10, 15 and 13–22 days post-hatch, at 28, 24, 20, and 17 °C, respectively. Importantly, exposure to cooler (17 °C) and warmer (28 °C) than optimal rearing temperatures (24 °C) in this species did not appear to increase CO2 sensitivity. Repeated experimentation documented substantial inter- and intra-experiment variability, highlighting the need for experimental replication to more robustly constrain inherently variable responses. Taken together, these results demonstrate that the early life stages of this ecologically important forage fish appear largely tolerate to even extreme levels of CO2 across a broad thermal regime.

Mercury bioaccumulation increases with latitude in a coastal marine fish (Atlantic silverside, Menidia menidia)

Human exposure to the neurotoxic methylmercury (MeHg) occurs primarily via the consumption of marine fish, but the processes underlying large-scale spatial variations in fish MeHg concentrations [MeHg], which influence human exposure, are not sufficiently understood. We used the Atlantic silverside (Menidia menidia), an extensively studied model species and important forage fish, to examine latitudinal patterns in total mercury (Hg) [Hg] and [MeHg]. Both [Hg] and [MeHg] significantly increased with latitude (0.014 and 0.048 μg MeHg·g dry weight−1 per degree of latitude in juveniles and adults, respectively). Four known latitudinal trends in silverside traits help explain these patterns: latitudinal increase in MeHg assimilation efficiency, latitudinal decrease in MeHg efflux, latitudinal increase in weight loss due to longer and more severe winters, and latitudinal increase in food consumption as an adaptation to decreasing length of the growing season. Given the absence of a latitudinal pattern in particulate MeHg, a diet proxy for zooplanktivorous fish, we conclude that large-scale spatial variation in growth is the primary control of Hg bioaccumulation in this and potentially other fish species.