Menidia Menidia Research Articles

The extraordinary Atlantic silverside and me

Abstract My career is inextricably linked to the remarkable characteristics and astonishing insights provided by a simple yet elegant species, the Atlantic silverside, Menidia menidia. My initial field and laboratory studies provided the first demonstration of temperature-dependent sex determination (TSD) and its adaptive significance in fish, as well as the first empirical confirmation of frequency-dependent sex ratio selection. This early work then led to the discovery of countergradient variation in growth, evolutionary trade-offs associated with growth, pioneered the study of fisheries-induced evolution, and furthered our understanding of the spatial scale of local adaptation in marine species. Most of these topics are now vigorous areas of research encompassing numerous species and systems. Here I describe how these unforeseen discoveries were made and led to other findings on bluefish (Pomatomus saltatrix) and striped bass (Morone saxatilis). An interest in leadership during my early years was later rekindled as I took on administrative roles. It all began with an intriguing observation stemming from my MS thesis that I was compelled to follow. My career illustrates the value of exploring deeply the natural history of lesser-known yet easy-to-study species and to follow unexpected observations even if peripheral to a preconceived plan of research.

Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside.

Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (Menidia menidia) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression, and the disruption of coexpression networks in hybrids point toward a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.

Effects of daily thermal fluctuations on the Atlantic silverside, a fish with temperature-dependent sex determination.

Temperature-dependent sex determination (TSD) occurs when the temperature during development affects gonad determination. Historically, most work on TSD in fishes was conducted under constant temperatures, yet daily fluctuating temperatures can significantly alter fish physiology and life history. Thus, we subjected the Atlantic silverside, Menidia menidia (a TSD species), to 28, 28 ± 2 and 28 ± 4°C (a high, masculinizing temperature) and quantified sex ratios and length. We found that the percentage of females increased by 60%-70% when the fish were exposed to daily fluctuating temperatures (from 10% to 16% and 17% under fluctuations).

COI amplicon sequence data of environmental DNA collected from the Bronx River Estuary, New York City

In this data paper, we describe environmental DNA (eDNA) cytochrome c oxidase (COI) amplicon sequence data from New York City’s Bronx River Estuary. As urban systems continue to expand, describing and monitoring their biodiversity is increasingly important for sustainability. Once polluted and overexploited, New York City’s Bronx River Estuary is undergoing revitalization and restoration. To investigate and characterize the area’s diversity, we collected and sequenced river sediment and surface water samples from Hunts Point Riverside and Soundview Parks (ntotal = 48; nsediment = 25; nwater = 23). COI analysis using universal primers mlCOIintF and jgHCO2198 detected 27,328 Amplicon Sequence Variants (ASVs) from 7,653,541 sequences, and rarefaction curves reached asymptotes indicating sufficient sampling depth. Of these, eukaryotes represented 9,841ASVs from 3,562,254 sequences. At the study sites over the sampling period, community composition varied by substrate (river sediment versus surface water) and with water temperature, but not pH. The three most common phyla were Bacillariophyta (diatoms), Annelida (segmented worms), and Ochrophyta (e.g. brown and golden algae). Of the eukaryotic ASVs, we identified 614 (6.2%) to species level, including several dinoflagellates linked to Harmful Algal Blooms such as Heterocapsa spp., as well as the invasive amphipod Grandidierella japonica. The analysis detected common bivalves including blue (Mytilus edulis) and ribbed (Geukensia demissa) mussels, as well as soft-shell clams (Mya arenaria), in addition to Eastern oysters (Crassostrea virginica) that are being reintroduced to the area. Fish species undergoing restoration such as river herring (Alosa pseudoharengus, A. aestivalis) failed to be identified, although relatively common fish including Atlantic silversides (Menidia menidia), menhaden (Brevoortia tyrannus), striped bass (Morone saxatilis), and mummichogs (Fundulus heteroclitus) were found. The data highlight the utility of eDNA metabarcoding for analyzing urban estuarine biodiversity and provide a baseline for future work in the area.

Comparative linkage mapping uncovers recombination suppression across massive chromosomal inversions associated with local adaptation in Atlantic silversides.

The role of recombination in genome evolution has long been studied in theory, but until recently empirical investigations had been limited to a small number of model species. Here, we compare the recombination landscape and genome collinearity between two populations of the Atlantic silverside (Menidia menidia), a small fish distributed across the steep latitudinal climate gradient of the North American Atlantic coast. We constructed separate linkage maps for locally adapted populations from New York and Georgia and their interpopulation laboratory cross. First, we used one of the linkage maps to improve the current silverside genome assembly by anchoring three large unplaced scaffolds to two chromosomes. Second, we estimated sex-specific recombination rates, finding 2.3-fold higher recombination rates in females than males-one of the most extreme examples of heterochiasmy in a fish. While recombination occurs relatively evenly across female chromosomes, it is restricted to only the terminal ends of male chromosomes. Furthermore, comparisons of female linkage maps revealed suppressed recombination along several massive chromosomal inversions spanning nearly 16% of the genome. These inversions segregate between locally adapted populations and coincide near perfectly with blocks of highly elevated genomic differentiation between wild populations. Finally, we discerned significantly higher recombination rates across chromosomes in the northern population compared to the southern. In addition to providing valuable resources for ongoing evolutionary and comparative genomic studies, our findings represent a striking example of structural variation that impacts recombination between adaptively divergent populations, providing empirical support for theorized genomic mechanisms facilitating adaptation despite gene flow.

Temperature-dependent effects on fecundity in a serial broadcast spawning fish after whole-life high CO2 exposure

AbstractExperiments examining fish sensitivities to future oceanic CO2 levels have greatly expanded over past decades and identified many potentially affected traits. Curiously, data on reproductive trait responses to high CO2 are still scarce, despite their strong link to Darwinian fitness and thus to population vulnerability to ocean acidification. We conducted two rearing experiments on the first broadcast-spawning marine fish model (Atlantic silverside, Menidia menidia) to examine how long-term and novel whole life-cycle exposures to predicted future CO2 levels (∼2,000 µatm) affect laboratory spawning, temperature-specific reproductive investment, fecundity, and size distributions of maturing oocytes. At low temperatures (17°C), female body size and therefore potential fecundity (FPot, oocytes/female) slightly increased with CO2, while relative fecundity (FRel, oocytes/g female) remained unaffected. At high temperatures (24°C), high CO2 substantially reduced both FPot (−19%) and FRel (−28%) relative to control treatments. Irrespective of CO2, females at 24°C grew larger and heavier than those at 17°C, and although larger females produced larger oocytes at some developmental stages, they also had lower gonadosomatic indices and lower FRel. Our findings contrast with most previous studies and thus highlight the need to investigate reproductive impacts of increasing CO2 on multiple fish species with contrasting life history strategies.

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 among the highest reported for a fish, or any vertebrate (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.

Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome.

The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median F ST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (F ST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.

The influence of nutrient loading on methylmercury availability in Long Island estuaries.

Estuaries provide critical habitat for food webs supporting fish and shellfish consumed by humans, but estuarine ecosystem health has been threatened by increases in nitrogen loading as well as inputs of the neurotoxin, mercury (Hg), which biomagnifies in food webs and poses risk to humans and wildlife. In this study, the effects of nutrient loading on the fate of Hg in shallow coastal estuaries were examined to evaluate if their interaction enhances or reduces Hg bioavailability in sediments, the water column, and concentrations in lower trophic level fish (Fundulus heteroclitus and Menidia menidia). Multiple sites were sampled within two human impacted coastal lagoons, Great South Bay (GSB) and Jamaica Bay (JB), on the southern coast of Long Island, NY, United States of America (U.S.A.). Carbon (C), nitrogen (N), sulfur (S), Hg, and methylmercury (MeHg) were measured in surface sediments and the water column, and total Hg (THg) was measured in two species of forage fish. Minimal differences were found in dissolved and particulate Hg, dissolved organic carbon (DOC), and salinity between the two bays. Across lagoons, concentrations of chlorophyll-a were correlated with total suspended solids (TSS), and water column THg and MeHg was largely associated with the particulate fraction. Methylmercury concentrations in particulates decreased with increasing TSS and chlorophyll-a, evidence of biomass dilution of MeHg with increasing productivity at the base of the food chain. Water column Hg was associated with THg concentrations in Atlantic silversides, while mummichog THg concentrations were related to sediment concentrations, reflecting their different feeding strategies. Finally, higher nutrient loading (lower C:N in sediments) while related to lower particulate concentrations coincided with higher bioaccumulation factors (BAF) for Hg in both fish species. Thus, in shallow coastal lagoons, increased nutrient loading resulted in decreased Hg concentrations at the base of the food web but resulted in greater bioaccumulation of Hg to fish relative to its availability in algal food.

Are long-term growth responses to elevated pCO2 sex-specific in fish?

Whether marine fish will grow differently in future high pCO2 environments remains surprisingly uncertain. Long-term and whole-life cycle effects are particularly unknown, because such experiments are logistically challenging, space demanding, exclude long-lived species, and require controlled, restricted feeding regimes-otherwise increased consumption could mask potential growth effects. Here, we report on repeated, long-term, food-controlled experiments to rear large populations (>4,000 individuals total) of the experimental model and ecologically important forage fish Menidia menidia (Atlantic silverside) under contrasting temperature (17°, 24°, and 28°C) and pCO2 conditions (450 vs. ~2,200 μatm) from fertilization to ~ a third of this annual species' life span. Quantile analyses of trait distributions showed mostly negative effects of high pCO2 on long-term growth. At 17°C and 28°C, but not at 24°C, high pCO2 fish were significantly shorter [17°C: -5 to -9%; 28°C: -3%] and weighed less [17°C: -6 to -18%; 28°C: -8%] compared to ambient pCO2 fish. Reductions in fish weight were smaller than in length, which is why high pCO2 fish at 17°C consistently exhibited a higher Fulton's k (weight/length ratio). Notably, it took more than 100 days of rearing for statistically significant length differences to emerge between treatment populations, showing that cumulative, long-term CO2 effects could exist elsewhere but are easily missed by short experiments. Long-term rearing had another benefit: it allowed sexing the surviving fish, thereby enabling rare sex-specific analyses of trait distributions under contrasting CO2 environments. We found that female silversides grew faster than males, but there was no interaction between CO2 and sex, indicating that males and females were similarly affected by high pCO2. Because Atlantic silversides are known to exhibit temperature-dependent sex determination, we also analyzed sex ratios, revealing no evidence for CO2-dependent sex determination in this species.

Isotopic Discrimination (δ15N, δ13C) in Captive and Wild Common Murres (Uria aalge) and Atlantic Puffins (Fratercula arctica).

Studying the diet of consumers using stable isotopes provides insight into the foraging ecology of individuals and species. To accurately reconstruct the integrated diet of animals using stable isotope values, we must quantify diet-tissue discrimination factors (DTDFs), or the way in which stable isotopes in prey are incorporated into the tissues of consumers. To quantify DTDFs, controlled experiments are needed, whereby consumers are fed a constant diet. However, relatively few controlled-diet studies have been conducted for seabirds. In this study, captive adult Atlantic puffins (Fratercula arctica) and common murres (Uria aalge) were fed a two-source diet of capelin (Mallotus villosus) and Atlantic silverside (Menidia menidia) to determine the DTDFs for the cellular component of blood and plasma for both δ15N and δ13C. The DTDFs for the cellular component (Δ15N: ; Δ13C: ) and plasma (Δ15N: ; Δ13C: ) of puffins were similar to those for the cellular component (Δ15N: ; Δ13C: ) and plasma (Δ15N: ; Δ13C: ) of murres. We reconstructed the diet of wild murres and puffins breeding on the northeastern coast of Newfoundland using previously published DTDFs and estimated DTDFs from our feeding experiment. Reconstructed dietary proportions supported a priori knowledge of diet, although outputs were sensitive to the DTDF used. Despite the similarity of our DTDFs for puffins and murres, along with the similarity of our DTDFs with those of other seabird species, our sensitivity analysis revealed considerable differences among resultant dietary contributions from mixing models, further highlighting the importance of using species- and tissue-specific DTDFs to enhance knowledge in the foraging ecology of seabirds using stable isotopes.

Acidification and hypoxia interactively affect metabolism in embryos, but not larvae, of the coastal forage fish Menidia menidia.

Ocean acidification is occurring in conjunction with warming and deoxygenation as a result of anthropogenic greenhouse gas emissions. Multistressor experiments are critically needed to better understand the sensitivity of marine organisms to these concurrent changes. Growth and survival responses to acidification have been documented for many marine species, but studies that explore underlying physiological mechanisms of carbon dioxide (CO2) sensitivity are less common. We investigated oxygen consumption rates as proxies for metabolic responses in embryos and newly hatched larvae of an estuarine forage fish (Atlantic silverside, Menidia menidia) to factorial combinations of CO2×temperature or CO2×oxygen. Metabolic rates of embryos and larvae significantly increased with temperature, but partial pressure of CO2 (PCO2 ) alone did not affect metabolic rates in any experiment. However, there was a significant interaction between PCO2 and partial pressure of oxygen (PO2 ) in embryos, because metabolic rates were unaffected by PO2 level at ambient PCO2 , but decreased with declining PO2 under elevated PCO2 For larvae, however, PCO2 and PO2 had no significant effect on metabolic rates. Our findings suggest high individual variability in metabolic responses to high PCO2 , perhaps owing to parental effects and time of spawning. We conclude that early life metabolism is largely resilient to elevated PCO2 in this species, but that acidification likely influences energetic responses and thus vulnerability to hypoxia.

A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries-induced evolution.

Natural selection is inherently a multivariate phenomenon. The selection pressure on size (natural and artificial) and the age at which selection occurs is likely to induce evolutionary changes in growth rates across the entire life history. However, the covariance structure that will determine the path of evolution for size at age has been studied in only a few fish species. We therefore estimated the genetic covariance function for size throughout ontogeny using Atlantic silversides (Menidia menidia) as the model system. Over a 3‐year period, a total of 542 families were used to estimate the genetic covariance in length at age from hatch through maturity. The function‐valued trait approach was employed to estimate the genetic covariance functions. A Bayesian hierarchical model was used to account for the unbalanced design, unequal measurement intervals, unequal sample sizes, and family‐aggregated data. To improve mixing, we developed a two‐stage sampler using a Gibbs sampler to generate the posterior of a well‐mixing approximate model followed by an importance sampler to draw samples from posterior of the completely specified model. We found that heritability of length is age‐specific and there are strong genetic correlations in length across ages that last 30 days or more. We used these estimates in a hypothetical model predicting the evolutionary response to harvesting following a single generation of selection under both sigmoidal and unimodal patterns of gear selectivity to illustrate the potential outcomes of ignoring the genetic correlations. In these scenarios, genetic correlations were found to have a strong effect on both the direction and magnitude of the response to harvest selection.

Otolith-based growth reconstructions in young-of-year Atlantic silversides Menidia menidia and their implications for sex-selective survival

Otolith-based growth reconstructions in young-of-year Atlantic silversides Menidia menidia and their implications for sex-selective survival

Finfish Diversity and Distribution in a Boreal, Macrotidal Bay

Cobscook Bay is an 11- km2 geographically complex, boreal, and macrotidal bay in eastern Maine. The physical environment, primary producers, and invertebrate assemblage of the bay are well-characterized, but no contemporary data exist on its finfish assemblage. We sampled the finfish assemblage of Cobscook Bay from 2011 to 2013 in May, June, August, and September to create a baseline dataset suitable for future comparisons. We also examined the composition, diversity, and annual changes in the assemblage. We sampled in the subtidal and intertidal zones using seines (n = 390), fyke nets (n = 72), and benthic (n = 112) and pelagic (n = 111) trawls; sampling was divided among the bay's 3 different sub-bays. We collected more than 60,000 individuals from 46 species. We employed species richness, Simpson's index of diversity, and non-metric multidimensional scaling (with the Bray—Curtis and Horn—Morisita indices) to examine spatial and temporal variation of finfish assemblages throughout the bay. Our analysis suggested that data collected in the subtidal pelagic were not a representative sample of that assemblage. Therefore, we considered 2 assemblages: the intertidal and subtidal benthic. Assemblage composition and species' relative abundances were different at diel, monthly, and annual timescales and were associated with changes in the catch rate of ubiquitous species. In the intertidal, these species included Gasterosteus aculeatus (Threespine Stickleback), Clupea harengus (Atlantic Herring), Alosa pseudoharengus (Alewife), and Menidia menidia (Atlantic Silverside). In the subtidal, the common species were Atlantic Herring and Pseudopleuronectes americanus (Winter Flounder). Statistical analyses indicated that both spatial and temporal factors were significant predictors of assemblage evenness. The sampling design, albeit complex, was sufficient to capture these differences and characterize these assemblages. Implications for future studies are that the study design must be sufficiently complex to capture the anticipated spatial and temporal variability inherent in such dynamic environments. Furthermore, given recent warming trends in the Gulf of Maine, this study's results suggest the importance of thoroughly understanding local temporal and ecosystem variability.

Robust quantification of fish early life CO2 sensitivities via serial experimentation.

Despite the remarkable expansion of laboratory studies, robust estimates of single species CO2 sensitivities remain largely elusive. We conducted a meta-analysis of 20 CO2 exposure experiments conducted over 6 years on offspring of wild Atlantic silversides (Menidia menidia) to robustly constrain CO2 effects on early life survival and growth. We conclude that early stages of this species are generally tolerant to CO2 levels of approximately 2000 µatm, likely because they already experience these conditions on diel to seasonal timescales. Still, high CO2 conditions measurably reduced fitness in this species by significantly decreasing average embryo survival (-9%) and embryo+larval survival (-13%). Survival traits had much larger coefficients of variation (greater than 30%) than larval length or growth (3-11%). CO2 sensitivities varied seasonally and were highest at the beginning and end of the species' spawning season (April-July), likely due to the combined effects of transgenerational plasticity and maternal provisioning. Our analyses suggest that serial experimentation is a powerful, yet underused tool for robustly estimating small but true CO2 effects in fish early life stages.

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.

Full mitochondrial genome sequences reveal new insights about post-glacial expansion and regional phylogeographic structure in the Atlantic silverside (Menidia menidia)

One of the biggest challenges in population genetics of marine species is to uncover subtle phylogeographic patterns masked by large effective population sizes and/or high gene flow. In this paper, we use 189 full mitochondrial genome sequences from the Atlantic silverside (Menidia menidia), obtained during whole nuclear genome re-sequencing, to address this challenge. With this approach, we were able to provide a high-resolution analysis of the demographic history and current genetic structure of the species. We clearly defined a regional genetic structure that is stronger than previously thought. This structure groups the species into three regional subdivisions: (1) south of Cape Cod; (2) Gulf of Maine; and (3) Gulf of St. Lawrence. Among the regional subdivisions, our data reveal that the two northern groups show the greatest divergence despite their adjacency along the latitudinal gradient, while genetic homogeneity within the southern subdivision suggests connectivity throughout its broad geographical distribution. Furthermore, using approximate Bayesian computation (ABC) methods, we inferred that both northern populations are the result of independent colonization events from the south after the Last Glacial Maximum (LGM). Our analyses indicate that at least one of the northern populations has received two waves of colonization, one timed immediately after the LGM and the other timed after the end of the Younger Dryas glacial re-advance. Finally, we found one locus potentially under positive selection in the mitochondrial genome. The results of this study illustrate the power of full mitochondrial genome sequencing in phylogeographic research, and because the Atlantic silverside is known for its clinal phenotypic variation throughout its range, our findings have important implications for the study of local adaptation.

Another useful property of mtDNA: editorial comment on the highlighted article by Lou et al. (2018)

Mitochondrial DNA (mtDNA) has been the marker of choice since the advent of phylogeography, and for good reasons. Foremost, mtDNA is haploid, i.e., represented by a single variant of the molecule, as opposed to two sets of nuclear chromosomes in diploid organisms. This reduces effective population size (Ne) by half compared to nuclear DNA, and also facilitates sequencing and genotyping (all base pairs are expected to be homozygous in a haploid marker, circumventing the need to identify and distinguish alleles in heterozygotes, either physically through cloning or bioinformatically). Furthermore, contrary to the nuclear genome that is transmitted by both parents, mtDNA is maternally inherited. This reduces Ne by another half, resulting in an expected Ne for mtDNA that is a fourth of nuclear DNA. Lower Ne results in stronger genetic drift, providing higher resolution for phylogeographic analysis. In the era of whole genome sequencing (WGS), these advantages of mtDNA are balanced by the much larger volume of data provided by the nuclear genome. Yet, another property of mtDNA is that cells typically harbor many copies of the mitochondrial genome versus just a few of the nuclear genome, resulting in higher sequencing coverage for mtDNA than for nuclear DNA. Lou et al. (2018) leveraged this property to recover the full mitochondrial genomes of 189 Atlantic silversides (Menidia menidia) at a mean coverage of 153× from a low-coverage (1.3×) WGS experiment (Therkildsen and Palumbi 2017). They carefully addressed a number of potential issues with mtDNA, including the fact that it is a circular molecule (which complicates mapping in the absence of edges) and the possibility of heteroplasmy (the occurrence of several mtDNA variants) or mitochondrial insertions into the nuclear DNA. The M. menidia mitochondrial genome was 16,454 base pairs long, providing significantly more data and phylogeographic resolution than an earlier Marine Biology study based on a 340 base pair segment of the mtDNA control region (Mach et al. 2011). It also provided the opportunity to search for signs of selection at the 13 protein-coding genes present in the mtDNA and apply approximate Bayesian computation (ABC) analysis for demographic inference. Yet notwithstanding its many advantages, mtDNA also comes with a number of limitations. One generalization emerging from whole genome analysis is that evolutionary histories vary along the genome. In this regard, as a single molecule that lacks recombination, mtDNA essentially behaves as—and provides a sample size of—one locus. A related matter is that in the presence of whole genome data, and particularly high-coverage data, the gain from adding mtDNA may be marginal unless there is a specific biological motivation to do so such as mito-nuclear interactions or sex-biased dispersal. The analysis of the nuclear genomic data will allow to establish to what extent this applies to M. menidia.

Starvation rates in larval and juvenile Atlantic silversides (Menidia menidia) are unaffected by high CO2 conditions

Over the past decade, laboratory experiments on fish early life stages have found many traits that are evidently sensitive to elevated CO2 levels. With respect to larval growth, high CO2 environments are commonly assumed to increase acid–base regulation and other plastic responses, thus incurring additional metabolic costs that reduce the scope for growth. This assumption is not well supported by empirical evidence. One reason might be that experiments often provide unrestricted feeding conditions, which could allow larvae to compensate for higher costs by increased food intake. To remove potentially confounding effects of larval feeding, we conducted a series of starvation trials on offspring of the Atlantic silverside (Menidia menidia), predicting faster starvation at high compared to ambient CO2 treatments. We compiled observations from five separate experiments spanning different years, laboratories, temperatures (17–26 °C), life stages (newly hatched larvae, previously fed larvae, early juveniles), and CO2 levels (300–6500 µatm). Contrary to expectation, we found that starvation rates were largely independent of the CO2 environment in this fish species. The one exception occurred at the lowest temperature and most extreme CO2 treatment, which resulted in slower not faster starvation in newly hatched larvae at high compared to ambient CO2 treatments. The apparent failure of starvation rate as a proxy for CO2 effects on larval fish metabolism may have several reasons, including potential CO2 tolerance of offspring, observed large stochasticity in early life survival masking small metabolic costs of high CO2, and the general depression and reconfiguration of fish metabolism in response to food deprivation.