Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs

The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (F_ST  = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.

Mature male parr contribution to the effective size of an anadromous Atlantic salmon (Salmo salar) population over 30 years

We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out-migrating smolt and post-spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Ne) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Ne estimates, suggesting that mature male parr are significantly increasing Nb and Ne over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.

Age structure, changing demography and effective population size in Atlantic salmon (Salmo salar)

Effective population size (N(e)) is a central evolutionary concept, but its genetic estimation can be significantly complicated by age structure. Here we investigate N(e) in Atlantic salmon (Salmo salar) populations that have undergone changes in demography and population dynamics, applying four different genetic estimators. For this purpose we use genetic data (14 microsatellite markers) from archived scale samples collected between 1951 and 2004. Through life table simulations we assess the genetic consequences of life history variation on N(e). Although variation in reproductive contribution by mature parr affects age structure, we find that its effect on N(e) estimation may be relatively minor. A comparison of estimator models suggests that even low iteroparity may upwardly bias N(e) estimates when ignored (semelparity assumed) and should thus empirically be accounted for. Our results indicate that N(e) may have changed over time in relatively small populations, but otherwise remained stable. Our ability to detect changes in N(e) in larger populations was, however, likely hindered by sampling limitations. An evaluation of N(e) estimates in a demographic context suggests that life history diversity, density-dependent factors, and metapopulation dynamics may all affect the genetic stability of these populations.

Population structure and gene flow reversals in Atlantic salmon (Salmo salar) over contemporary and long-term temporal scales: effects of population size and life history

Metapopulation dynamics are increasingly invoked in management and conservation of endangered species. In this context, asymmetrical gene flow patterns can be density dependent, with migration occurring mainly from larger into smaller populations, which may depend on it for their persistence. Using genetic markers, such patterns have recently been documented for various organisms including salmonids, suggesting this may be a more general pattern. However, metapopulation theory does not restrict gene flow asymmetry to 'source-sink' structures, nor need these patterns be constant over longer evolutionary timescales. In anadromous salmonids, gene flow can be expected to be shaped by various selective pressures underlying homing and dispersal ('straying') behaviours. The relative importance of these selective forces will vary spatially and for populations of different census size. Furthermore, the consequences of life-history variation among populations for dispersal and hence gene flow remain poorly quantified. We examine population structure and connectivity in Atlantic salmon (Salmo salar L.) from Newfoundland and Labrador, a region where populations of this species are relatively pristine. Using genetic variation at 13 microsatellite loci from samples (N=1346) collected from a total of 20 rivers, we examine connectivity at several regional and temporal scales and test the hypothesis that the predominant direction of gene flow is from large into small populations. We reject this hypothesis and find that the directionality of migration is affected by the temporal scale over which gene flow is assessed. Whereas large populations tend to function as sources of dispersal over contemporary timescales, such patterns are often changed and even reversed over evolutionary, coalescent-derived timescales. These patterns of population structure furthermore vary between different regions and are compatible with demographic and life-history attributes. We find no evidence for sex-biased dispersal underlying gene flow asymmetry. Our findings caution against generalizations concerning the directionality of gene flow in Atlantic salmon and emphasize the need for detailed regional study, if such information is to be meaningfully applied in conservation and management of salmonids.

Quantitative scanning transmission electron microscopy of ultrathin cryosections: subcellular organelles in rapidly frozen liver and cerebellar cortex

Freeze-dried, ultrathin cryosections of directly frozen mouse liver and brain have been prepared and characterized by low-dose dark-field scanning transmission electron microscopy (STEM). These improved cryosections gave images comparable to those from conventional plastic sections. They were thin enough (< < 1.0 elastic mean free path) to use established dark-field techniques, modified for thickness-dependent nonlinearities, to measure the dry mass fraction of individual organelles, and hence to deduce their water content. Digital STEM imaging in combination with electron and X-ray spectroscopy has important biological applications, as illustrated by studies on calcium regulation in Purkinje neurons. Calcium concentrations per unit dry weight of dendritic compartments were determined by the peak/continuum method of energy-dispersive X-ray spectroscopy (EDXS), which necessarily overstates elemental concentrations because of beam-induced mass loss. The dry mass content of organelles at low dose and the percentage of dry mass retained after analysis at high dose were as follows: mitochondria (46.0 g dry mass/100 g hydrated mass, 67% mass retained); endoplasmic reticulum (27.9 g/100 g, 57%); and cytoplasm (16.3 g/100 g, 41%). These values were used to correct elemental concentrations for mass loss. Results indicated that the major calcium storage organelle in Purkinje cell dendrites is the endoplasmic reticulum, of which there are two types distinguished by their levels of calcium. Parallel electron energy loss spectroscopy of dendritic organelles corroborated EDXS measurements, with an improved sensitivity that indicates the feasibility of quantitative calcium mapping.

Facial electromyography as a predictor of treatment outcome in depression

Electromyograms (EMGs) from the corrugator, zygomatic and splenius capitis muscle sites and Beck depression inventory scores were obtained from 21 depressed in-patients shortly after admission and after two weeks in hospital. Contrary to the result of a previous study by other investigators, significant covariaton between depressive symptoms and corrugator EMG levels was not seen. However, consistent with a second finding of the previous study, initial corrugator EMG levels were shown to be significantly predictive of treatment outcome. Further, initial EMG from the zygomatic was also found to predict changes in depression. The explanation is unclear and further research is needed.

Autoshaping and food acquisition in mice: a genetic analysis

A genetic analysis was undertaken for a number of quantitative behavioral characters that were hypothesized to be components in a generalized feeding pattern. These measures included open-field activity, rate of food ingestion, and rate of development of an autoshaped operant response. Four strains of inbred laboratory mice were used as subjects in a diallel cross design. Standard analytical procedures, including the Hayman analysis of variance and the Jinks variance-covariance diagram, were used to interpret the data. The results were evaluated in terms of the contribution of fitness provided by each of the measured characters. It is concluded that both the various open-field measures and the food-consumption measure were of some importance in the evolutionary history of the mouse. The autoshaping measures, on the other hand, showed a pattern of inheritance that differed from the other measures and offered no clear interpretation of their evolutionary significance.