Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife.

Comparative approaches in physiological genomics offer an opportunity to understand the functional importance of genes involved in niche exploitation. We used populations of Alewife (Alosa pseudoharengus) to explore the transcriptional mechanisms that underlie adaptation to fresh water. Ancestrally anadromous Alewives have recently formed multiple, independently derived, landlocked populations, which exhibit reduced tolerance of saltwater and enhanced tolerance of fresh water. Using RNA-seq, we compared transcriptional responses of an anadromous Alewife population to two landlocked populations after acclimation to fresh (0 ppt) and saltwater (35 ppt). Our results suggest that the gill transcriptome has evolved in primarily discordant ways between independent landlocked populations and their anadromous ancestor. By contrast, evolved shifts in the transcription of a small suite of well-characterized osmoregulatory genes exhibited a strong degree of parallelism. In particular, transcription of genes that regulate gill ion exchange has diverged in accordance with functional predictions: freshwater ion-uptake genes (most notably, the 'freshwater paralog' of Na+ /K+ -ATPase α-subunit) were more highly expressed in landlocked forms, whereas genes that regulate saltwater ion secretion (e.g. the 'saltwater paralog' of NKAα) exhibited a blunted response to saltwater. Parallel divergence of ion transport gene expression is associated with shifts in salinity tolerance limits among landlocked forms, suggesting that changes to the gill's transcriptional response to salinity facilitate freshwater adaptation.

Nearshore energy subsidies support Lake Michigan fishes and invertebrates following major changes in food web structure.

Aquatic food webs that incorporate multiple energy channels (e.g., nearshore benthic and pelagic) with varying productivity and turnover rates convey stability to biological communities by providing independent energy sources. Within the Lake Michigan food web, invasive dreissenid mussels have caused rapid changes to food web structure and potentially altered the channels through which consumers acquire energy. We used stable C and N isotopes to determine how Lake Michigan food web structure has changed in the past decade, coincident with the expansion of dreissenid mussels, decreased pelagic phytoplankton production, and increased nearshore benthic algal production. Fish and invertebrate samples collected from sites around Lake Michigan were analyzed to determine taxa-specific 13C:12C (delta13C) and 15N:14N (delta15N) ratios. Sampling took place during two distinct periods, 2002-2003 and 2010-2012, that spanned the period of dreissenid expansion, and included nearshore, pelagic and profundal fish and invertebrate taxa. The magnitude and direction of the delta13C shift indicated significantly greater reliance upon nearshore benthic energy sources among nearly all fish taxa as well as profundal invertebrates following dreissenid expansion. Although the mechanisms underlying this delta13C shift likely varied among species, possible causes include the transport of benthic algal production to offshore waters and increased feeding on nearshore prey items by pelagic and profundal species. delta15N shifts were more variable and of smaller magnitude across taxa, although declines in delta15N among some pelagic fishes suggest a shift to alternative prey resources. Lake Michigan fishes and invertebrates appear to have responded to dreissenid-induced changes in nutrient and energy pathways by switching from pelagic to alternative nearshore energy subsidies. Although large shifts in energy allocation (i.e., pelagic to nearshore benthic) resulting from invasive species appear to affect total production at upper trophic levels, changes in trophic structure and utilization of novel energy pathways may help to stabilize food webs following species invasions.

Effects of dietary vitamin B1 (thiamine) and magnesium on the survival, growth and histological indicators in lake trout (Salvelinus namaycush) juveniles.

An interaction of two essential nutrients, thiamine and magnesium (Mg) has been documented in in vitro and in vivo studies in mammalian metabolism. However, the role of this association in poikilothermic vertebrates, such as fish, remains elusive. The purpose of this study was first to investigate the effects of dietary thiamine and Mg, and their interaction in lake trout and second to better understand the mechanism leading to early mortality syndrome (EMS), which is caused by a low thiamine level in embryos of many species of salmonids in the wild. Semi-purified diets (SPD) were prepared to accomplish 2 × 2 factorial design that were either devoid of or supplemented with thiamine mononitrate (20 mg/kg diet), magnesium oxide (700 mg/kg diet), or both. Lake trout alevins at the swim-up stage were fed for 10 wk one of the SPD diets or a commercial diet at the same rate (2.0-1.5%) based on recorded biomass. Our results showed that the concentrations of thiamine in the trunk muscle and Mg of whole body were closely associated with the dietary level of two nutrients. The interaction of low dietary Mg and thiamine resulted in apparently worsened overt symptoms of thiamine deficiency in lake trout leading to a higher mortality of fish during the seven week long trial (P<0.05). The fish fed a thiamine-devoid and Mg-supplemented diet were presumed to survive longer (10 wk) than the fish fed diets devoid of both nutrients (discontinued after 7th wk due to high mortality). However, we did not observe histopathological changes in the brain and liver corresponding to thiamine concentrations in tissues. These data suggest that Mg enhanced utilization of the thiamine remaining in the fish body and its interdependence was consistent with observations in mammals. EMS severity might be worsened when Mg is deficient in parental diets (and consequently in yolk sac) and/or first feed.

Effects of vitamin B1 (thiamine) deficiency in lake trout (Salvelinus namaycush) alevins at hatching stage.

The objectives of this study were to examine the relationship between thiamine concentrations in unfertilized eggs and yolksac individuals of lake trout (Salvelinus namaycush), along with any associated histopathological changes in the tissues of alevins at the hatching stage. We address these questions in a lake trout population from different spawning grounds of Lake Michigan (North and South), known for compromised survival due to early mortality syndrome (EMS). However, a dichotomous forage base of lake trout spawning stocks, with a dietary thiaminase-rich alewife in the North, and dietary low-thiaminase round goby in the South, provides the basis for the assumption that different diets may lead to differences in severity of EMS between different stocks. Lake trout eggs of 18 females were collected and fertilized individually with the sperm of several males. The eggs, eyed embryos and newly-hatched alevins were sampled to examine thiamine utilization during embryogenesis. Progenies of females with low (< 0.73 nmol/g) and high (> 0.85 nmol/g) levels of thiamine were chosen for histological studies. The obtained results showed that total thiamine levels in the body and yolk of eyed embryos and alevins at hatching were influenced by thiamine levels of unfertilized eggs and it decreased during embryogenesis (to 51% in eyed embryos and 28% in newly-hatched alevins in comparison to unfertilized eggs). The survival of lake trout until hatching stage does not correlate with the thiamine level, however it was affected by collection site and was significantly higher in fish from the South site (Julian's Reef). At the hatching stage, no pathological changes were observed in the brain, olfactory lobe, retina or liver in embryos regardless of thiamine concentrations in unfertilized eggs. It has been concluded that an enhanced thiamine requirement for the fast muscle mass growth near the swim-up stage is responsible for overt and histopathological signs of EMS. Current study confirms earlier findings that lake trout suffering from EMS can be successfully treated by immersion in thiamine solution as late as at the swim-up stage.

Species identity matters when interpreting trophic markers in aquatic food webs.

In aquatic systems, food web linkages are often assessed using diet contents, stable isotope ratios, and, increasingly, fatty acid composition of organisms. Some correlations between different trophic metrics are assumed to be well-supported; for example, particular stable isotope ratios and fatty acids seem to reflect reliance on benthic or pelagic energy pathways. However, understanding whether the assumed correlations between different trophic metrics are coherent and consistent across species represents a key step toward their effective use in food web studies. To assess links among trophic markers, we compared relationships between major diet components, fatty acids, and stable isotope ratios in three fishes: yellow perch (Perca flavescens), round goby (Neogobius melanostomus), and spottail shiner (Notropis hudsonius) collected from nearshore Lake Michigan. Yellow perch and spottail shiner are native in this system, while round goby are a relatively recent invader. We found some evidence for agreement between different trophic metrics, especially between diet components, n-3:n-6 fatty acid ratios, and stable isotope ratios (δ13C and δ15N). However, we also observed significant variation in observed relationships among markers and species, potentially due to taxonomic variation in the specific diet items consumed (e.g., chydorid microcrustaceans and Dreissena mussels) and species-specific biochemical processes. In many of these latter cases, the invasive species differed from the native species. Understanding the effects of taxonomic variation on prey and predator signatures could significantly improve the usefulness of fatty acids in food web studies, whereas diet contents and stable isotopes appear to be reliable indicators of trophic niche in aquatic food webs.

Beta-thymosin gene polymorphism associated with freshwater invasiveness of alewife (Alosa pseudoharengus).

Predicting the success of a species' colonization into a novel environment is routinely considered to be predicated on niche-space similarity and vacancy, as well as propagule pressure. The role genomic variation plays in colonization success (and the interaction with environment) may be suggested, but has not rigorously been documented. To test an hypothesis that previously observed ecotype-specific polymorphisms between anadromous and landlocked alewife (Alosa pseudoharengus) populations are an adaptive response to osmoregulatory challenges rather than a result of allele sampling at founding, we examined multiple anadromous and landlocked (colonized) populations for their allelic profiles at a conserved region (3'-UTR end) of a ß-thymosin gene whose protein product plays a central role in the organization of cytoskeleton. The putatively ancestral ß-thymosin allele was prevalent in anadromous populations, whereas a newly derived allele was overrepresented in landlocked populations; a third allele was exclusive to the anadromous populations. We also conducted a complementary set of salinity exposure experiments to test osmoregulatory performance of the alewife ecotypes in contrasting saline environments. The pattern of variation and results from these challenges indicate a strong association of ß-thymosin with colonization success and a transition from species with an anadromous life history to one with only a freshwater component.

Genetic divergence between freshwater and marine morphs of alewife (Alosa pseudoharengus): a 'next-generation' sequencing analysis.

Alewife Alosa pseudoharengus, a small clupeid fish native to Atlantic Ocean, has recently (∼150 years ago) invaded the North American Great Lakes and despite challenges of freshwater environment its populations exploded and disrupted local food web structures. This range expansion has been accompanied by dramatic changes at all levels of organization. Growth rates, size at maturation, or fecundity are only a few of the most distinct morphological and life history traits that contrast the two alewife morphs. A question arises to what extent these rapidly evolving differences between marine and freshwater varieties result from regulatory (including phenotypic plasticity) or structural mutations. To gain insights into expression changes and sequence divergence between marine and freshwater alewives, we sequenced transcriptomes of individuals from Lake Michigan and Atlantic Ocean. Population specific single nucleotide polymorphisms were rare but interestingly occurred in sequences of genes that also tended to show large differences in expression. Our results show that the striking phenotypic divergence between anadromous and lake alewives can be attributed to massive regulatory modifications rather than coding changes.

Linking egg thiamine and fatty acid concentrations of Lake Michigan lake trout with early life stage mortality.

The natural reproduction of lake trout Salvelinus namaycush in Lake Michigan is thought to be compromised by nutritional deficiency associated with inadequate levels of thiamine (vitamin B1) in their eggs. However, mortality driven by thiamine deficiency (commonly referred to as early mortality syndrome [EMS]) is not the only significant cause of low lake trout survival at early life stages. In this study, we sought to better understand the combined effects of variable levels of thiamine and fatty acids in lake trout eggs on prehatch, posthatch, and swim-up-stage mortality. We sampled the eggs of 29 lake trout females from southwestern Lake Michigan. The concentrations of free thiamine and its vitamers (e.g., thiamine monophosphate [TMP] and thiamine pyrophosphate [TPP]) as well as fatty acid profiles were determined in sampled eggs. Fertilized eggs and embryos were monitored through the advanced swim-up stage (1,000 degree-days). Three distinct periods of mortality were identified: prehatch (0-400 degree-days), immediately posthatch (401-600 degree-days), and swim-up (601-1,000 degree-days). Stepwise multiple regression analysis revealed (1) that cis-7-hexadecenoic acid in both neutral lipids (NL) and phospholipids (PL) correlated with prehatch mortality, (2) that docosapentaenoic acid in PL and docosahexaenoic acid in NL correlated with posthatch mortality, and (3) that total lipids, TPP, and palmitoleic acid in NL, linoleic acid, and palmitic acid in PL correlated with the frequency of EMS. These results indicate the complexity of early life stage mortality in lake trout and suggest that inadequate levels of key fatty acids in eggs, along with variable thiamine content, contribute to the low survival of lake trout progeny in Lake Michigan.

Molecular markers of yolk sac fry development in nine families of lake trout.

Salmonids in certain areas of North America and northern Europe suffer from reproductive disturbances manifested through the death of yolk sac fry. These disturbances are referred to as early mortality syndrome (EMS) in the Great Lakes region and M74 in the Baltic Sea. Both of these syndromes have been associated with reduced concentrations of thiamine in affected females and their eggs. However, large variations in signs and mortality, both within and between the individual syndromes, have been reported. Yolk sac fry mortality (M74) in Atlantic salmon Salmo salar has been shown to be associated with reduced DNA binding of the hypoxia-inducible transcription factor 1 (HIF-1), reduced production of vascular endothelial growth factor (VEGF) protein, decreased capillary density, and down-regulation of adult-type globin gene transcription (which is responsible for the protein part of adult hemoglobin). One of the main effects of all of these changes is reduced oxygen transport to the tissues of affected fry. In this study, the developmental patterns of HIF-1 DNA binding, VEGF protein expression, and adult-type globin gene transcription were analyzed in nine family groups of Lake Michigan lake trout Salvelinus namaycush. The results indicate that HIF-1 DNA binding and globin gene transcription increase from hatch to the end of yolk sac stage. Interindividual and between-family biological variations were detected, especially in VEGF protein expression and globin gene transcription. Our results demonstrate the possibility of using these molecular markers in investigating the etiology of EMS and making comparisons between the mechanisms of different salmonid yolk sac fry mortalities.

Effects of vitamin B1 (thiamine) deficiency in lake trout alevins and preventive treatments.

The objectives of this study were to examine the effect of thiamine immersion of fish from a population known for compromised survival as a result of early mortality syndrome (EMS) and to investigate the cause-response relationship between thiamine concentration and lesions in tissues in swim-up-stage lake trout Salvelinus namaycush alevins. Lake trout eggs from 14 fish from Lake Michigan were artificially fertilized and the progeny divided into two groups based on the thiamine concentration (low [< 0.73 nmol/g] or high [> 0.85 nmol/g]) in the unfertilized eggs. Progeny were treated or not with a thiamine solution (2,000 mg/L for 2 h) at hatching or the swim-up stage. The survival of progeny in control groups at the swim-up stage correlated with thiamine concentration. The low thiamine-treated groups had significantly higher survival between the swim-up stage (812.0 degree-days) and 16 d after swim-up (963.3 degree-days) than the control groups; the survival of the high thiamine-treated groups did not differ between treated and control fish, regardless of the treatment at hatching and the swim-up stage. Control alevins that had low thiamine levels showed EMS, which resulted in 94.9-100% mortality 16 d after the swim-up stage. No pathological changes were observed in the brain, olfactory lobe, eye, liver, or muscle in alevins of high thiamine-treated group. Glycogen deposits in the liver of alevins from the low control group were variable, no glycogen being observed in the hepatocytes of 7 of the 24 fish. We demonstrate that thiamine treatment at swim-up enhances the survival of EMS-affected lake trout relative to treatment at hatching.