Body length changes for Atlantic salmon (Salmo salar) over five decades exhibit weak spatial synchrony over a broad latitudinal gradient.

Understanding the factors that drive spatial synchrony among populations or species is important for management and recovery of populations. The range-wide declines in Atlantic salmon (Salmo salar) populations may be the result of broad-scale changes in the marine environment. Salmon undergo rapid growth in the ocean; therefore changing marine conditions may affect body size and fecundity estimates used to evaluate whether stock reference points are met. Using a dataset that spanned five decades, 172,268 individuals, and 19 rivers throughout Eastern Canada, we investigated the occurrence of spatial synchrony in changes in the body size of returning wild adult Atlantic salmon. Body size was then related to conditions in the marine environment (i.e., climate indices, thermal habitat availability, food availability, density-dependence, and fisheries exploitation rates) that may act on all populations during the ocean feeding phase of their life cycle. Body size increased during the 1980s and 1990s for salmon that returned to rivers after one (1SW) or two winters at sea (2SW); however, significant changes were only observed for 1SW and/or 2SW in some mid-latitude and northern rivers (10/13 rivers with 10 of more years of data during these decades) and not in southern rivers (0/2), suggesting weak spatial synchrony across Eastern Canada. For 1SW salmon in nine rivers, body size was longer when fisheries exploitation rates were lower. For 2SW salmon, body size was longer when suitable thermal habitat was more abundant (significant for 3/8 rivers) and the Atlantic Multidecadal Oscillation was higher (i.e., warmer sea surface temperatures; significant for 4/8 rivers). Overall, the weak spatial synchrony and variable effects of covariates on body size across rivers suggest that changes in Atlantic salmon body size may not be solely driven by shared conditions in the marine environment. Regardless, body size changes may have consequences for population management and recovery through the relationship between size and fecundity.

Divergence in Reproductive Behaviors Is Associated with the Evolutionary Loss of Parental Care.

AbstractThe mechanisms underlying the divergence of reproductive strategies between closely related species are still poorly understood. Additionally, it is unclear which selective factors drive the evolution of reproductive behavioral variation and how these traits coevolve, particularly during early divergence. To address these questions, we quantified behavioral differences in a recently diverged pair of Nova Scotian three-spined stickleback (Gasterosteus aculeatus) populations, which vary in parental care, with one population displaying paternal care and the other lacking this. We compared both populations, and a full reciprocal F1 hybrid cross, across four major reproductive stages: territoriality, nesting, courtship, and parenting. We identified significant divergence in a suite of heritable behaviors. Importantly, F1 hybrids exhibited a mix of behavioral patterns, some of which suggest sex linkage. This system offers fresh insights into the coevolutionary dynamics of reproductive behaviors during early divergence and offers support for the hypothesis that coevolutionary feedback between sexual selection and parental care can drive rapid evolution of reproductive strategies.

Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma.

BACKGROUND: Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural variants, which has not previously been tested in neuroblastoma. We used OGM to identify copy number and structural variants (SVs) in neuroblastoma which may have been missed by standard cytogenetic techniques. METHODS: Five neuroblastoma cell lines (SH-SY5Y, NBLW, GI-ME-N, NB1691 and SK-N-BE2(C)) and two neuroblastoma tumours were analysed using OGM with the Bionano Saphyr® instrument. The results were analysed using Bionano Access software and compared to previous genetic analyses including G-band karyotyping, FISH (fluorescent in situ hybridisation), single-nucleotide polymorphism (SNP) array and RNA fusion panels for cell lines, and SNP arrays and whole genome sequencing (WGS) for tumours. RESULTS: OGM detected copy number abnormalities found using previous methods and provided estimates for absolute copy numbers of amplified genes. OGM identified novel SVs, including fusion genes in two cell lines of potential clinical significance. CONCLUSIONS: OGM can reliably detect clinically significant structural and copy number variations in a single test. OGM may prove to be more time- and cost-effective than current standard cytogenetic techniques for neuroblastoma.

Does paternal care influence mate preference? Male and female mating behavior in Threespine Stickleback ecotypes that differ markedly in parental care.

Reproductive isolation can occur due to divergence in sexual selection for particular traits. For example, differences in mate preference associated with body size can play an important role in divergence between groups. The importance of mate preference for population divergence may be influenced by other aspects of a mating system, such as the requirement for parental care. In Nova Scotia, Canada, two ecotypes of marine Threespine Stickleback occur sympatrically: a "common" ecotype wherein males provide parental care, and a "white" ecotype that does not exhibit paternal care. The goal of our study was to examine differences in male mate preference between white and common stickleback males to test the prediction that males who invest more in parental care may be more selective about their mates. Because of the link between size and fecundity in this species, we predict that males that invest in parental care should prefer large females, while males that do not provide care will not exhibit preference for larger female size. We found that common male stickleback preferred larger-bodied females of both ecotypes, while white males showed a preference for larger-bodied common females. Secondarily, we assessed whether females differed in their willingness to mate with males of different sizes and ecotypes. Common female stickleback had a higher response rate toward smaller white males, which may be associated with their relatively high courtship rates. Counter to previous studies on these ecotypes that suggest that mating is completely assortative, interecotype matings occurred in half of the observed spawning events. This observation, coupled with the results that males may prefer females based mainly on size and females respond to males who court more rigorously regardless of their ecotype, may lend insight into recent genetic evidence for hybridization in the wild.

Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.).

When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and F. diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀ × H♂). To determine why F. heteroclitus × F. diaphanus F1 hybrids (H♀ × D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference and male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, whereas F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀ × D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀ × H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀ × H♂ crosses had a higher hatching success than F. diaphanus crosses at 10 ppt, which may further increase their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.

Dependents as Signals of Mate Value: Long-term Mating Strategy Predicts Displays on Online Dating Profiles for Men.

Sexual strategies theory indicates women prefer mates who show the ability and willingness to invest in a long-term mate due to asymmetries in obligate parental care of children. Consequently, women's potential mates must show they can provide investment - especially when women are seeking a long-term mate. Investment may be exhibited through financial and social status, and the ability to care for a mate and any resulting offspring. Men who care for children and pets (hereafter "dependents") are perceived as high-quality mates, given that dependents signal an ability to invest; however, no studies have examined how dependents are associated with short-term and long-term mating strategies. Here, online dating profiles were used to test the predictions that an interactive effect between sex and mating strategy will predict displays of dependents, with long-term mating strategy predicting for men but not women. Moreover, this pattern should hold for all dependent types and, due to relative asymmetries in required investment, differences will be strongest regarding displays of children and least in non-canine pets. As expected, men seeking long-term mates displayed dependents more than men seeking short-term mates, but both men and women seeking long-term mates displayed dependents similarly. This pattern was driven mostly by canines. These findings indicate that men adopting a long-term mating strategy display their investment capabilities more compared to those seeking short-term mates, which may be used to signal their mate value.

Short-term cold stress and heat shock proteins in the crustacean Artemia franciscana.

In their role as molecular chaperones, heat shock proteins (Hsps) mediate protein folding thereby mitigating cellular damage caused by physiological and environmental stress. Nauplii of the crustacean Artemia franciscana respond to heat shock by producing Hsps; however, the effects of cold shock on Hsp levels in A. franciscana have not been investigated previously. The effect of cold shock at 1 °C followed by recovery at 27 °C on the amounts of ArHsp90, Hsp70, ArHsp40, and ArHsp40-2 mRNA and their respective proteins in A. franciscana nauplii was examined by quantitative PCR (qPCR) and immunoprobing of western blots. The same Hsp mRNAs and proteins were also quantified during incubation of nauplii at their optimal growth temperature of 27 °C. qPCR analyses indicated that the abundance of ArHsp90, Hsp70, and ArHsp40 mRNA remained relatively constant during both cold shock and recovery and was not significantly different compared with levels at optimal temperature. Western blotting revealed that ArHsp90, ArHsp40, and ArHsp40-2 were generally below baseline, but at detectable levels during the 6 h of cold shock, and persisted in early recovery stages before declining. Hsp70 was the only protein that remained constant in quantity throughout cold shock and recovery. By contrast, all Hsps declined rapidly during 6 h when nauplii were incubated continuously at 27 °C optimal temperature. Generally, the amounts of ArHsp90, ArHsp40, and ArHsp40-2 were higher during cold shock/recovery than those during continuous incubation at 27 °C. Our data support the conclusion that low temperature preserves Hsp levels, making them available to assist in protein repair and recovery after cold shock.

Fisheries-induced evolution of alternative male life history tactics in Coho salmon.

Fisheries-induced evolution (FIE) can result when harvest imposes artificial selection on variation in heritable phenotypic traits. While there is evidence for FIE, it remains difficult to disentangle the contributions of within-generation demographic adjustment, phenotypic plasticity, and genetic adaption to observed changes in life history traits. We present evidence for FIE using dozens of Coho salmon (Oncorhynchus kisutch) populations in which males adopt one of two age-invariant, heritable life history tactics: most mature as large three-year-old "hooknose" and typically fight for spawning opportunities, while some mature as small two-year-old "jacks" and fertilize eggs through sneaking. The closure of a fishery targeting three-year-old fish provided an experimental test of the prediction that fishery-imposed selection against hooknose males drives an evolutionary increase in the proportion of males adopting the jack tactic. The data support the prediction: 43 of 46 populations had higher jack proportions during than after the fishery. The data further suggest that changes in jack proportion were not solely the result of demographic adjustments to harvest. We suggest that systems where fisheries differentially exploit phenotypically discrete, age-invariant life histories provide excellent opportunities for detecting FIE.

Small changes, big gains: A curriculum-wide study of teaching practices and student learning in undergraduate biology.

A growing body of evidence has shown that active learning has a considerable advantage over traditional lecture for student learning in undergraduate STEM classes, but there have been few large-scale studies to identify the specific types of activities that have the greatest impact on learning. We therefore undertook a large-scale, curriculum-wide study to investigate the effects of time spent on a variety of classroom activities on learning gains. We quantified classroom practices and related these to student learning, assessed using diagnostic tests written by over 3700 students, across 31 undergraduate biology classes at a research-intensive university in the Pacific Northwest. The most significant positive predictor of learning gains was the use of group work, supporting the findings of previous studies. Strikingly, we found that the addition of worksheets as an active learning tool for in-class group activities had the strongest impact on diagnostic test scores. This particular low-tech activity promotes student collaboration, develops problem solving skills, and can be used to inform the instructor about what students are struggling with, thus providing opportunities for valuable and timely feedback. Overall, our results indicate that group activities with low barriers to entry, such as worksheets, can result in significant learning gains in undergraduate science.

Retention following Two-Stage Collaborative Exams Depends on Timing and Student Performance.

Multistage collaborative exams are implemented to enhance learning and retention of course material. However, the effects of multistage collaborative exams on retention of course content are varied. These discrepancies may be due to a number of factors. To date, studies examining collaborative exams and content retention have used questions that all, or mostly, require students to select an answer, rather than generate one of their own. However, content retention can improve when students generate their own responses. Thus, we examined the effect of collaborative exams with open-ended questions on retention of course content. Retention was measured at two time periods; one relatively shortly (9 days) following a collaborative exam and another over a longer time period (23 days). Furthermore, we examined whether content retention differed for low-, mid-, or high--performing students. Our results suggest that collaborative exams offer retention benefits at relatively long time periods between pre- and posttests, but not over shorter time periods. Retention varied across students in different performance categories. Our study, the first to use only open-ended questions, showed relatively small effects compared with studies using multiple-choice or fill-in-the-blank format, but still suggest that collaborative exams can aid in content retention.

Sub-lethal viral exposure and growth on drought stressed host plants changes resource allocation patterns and life history costs in the Speckled Wood butterfly, Pararge aegeria.

This study investigated the interactive effects of growth on drought stressed host plants and pathogen challenge with the baculovirus Autographa californica nucleopolyhedrovirus (AcMNPV) on survival and fitness-related traits using the Speckled Wood butterfly, Pararge aegeria (L.). Exposure to AcMNPV significantly reduced survival to pupation. For surviving larvae, sub-lethal infection significantly decreased daily mass acquisition rates and pupal mass. Growth on drought stressed plants increased daily mass acquisition rates resulting in heavier pupae, and increased resource allocation to adult reproduction. The interaction between host plant drought and viral exposure resulted in different resource allocation strategies, and thus different growth trajectories, between larvae. This in turn resulted in significantly different allometric relationships between larval mass (at inoculation) and both development time and investment in flight muscles. For larvae with relatively lighter masses there was a cost of resisting infection when growth occurred on drought stressed host plants, both within the larval stage (i.e. longer larval development times) and in the adult stage (i.e. lower investment in flight muscle mass). This multi-factor study highlights several potential mechanisms by which the complex interplay between low host plant nutritional quality due to drought, and pathogen exposure, may differentially influence the performance of P. aegeria individuals across multiple life stages.

The evolutionary consequences of habitat fragmentation: Body morphology and coloration differentiation among brook trout populations of varying size.

A reduction in population size due to habitat fragmentation can alter the relative roles of different evolutionary mechanisms in phenotypic trait differentiation. While deterministic (selection) and stochastic (genetic drift) mechanisms are expected to affect trait evolution, genetic drift may be more important than selection in small populations. We examined relationships between mature adult traits and ecological (abiotic and biotic) variables among 14 populations of brook trout. These naturally fragmented populations have shared ancestry but currently exhibit considerable variability in habitat characteristics and population size (49 < Nc < 10,032; 3 < Nb < 567). Body size, shape, and coloration differed among populations, with a tendency for more variation among small populations in both trait means and CV when compared to large populations. Phenotypic differences were more frequently and directly linked to habitat variation or operational sex ratio than to population size, suggesting that selection may overcome genetic drift at small population size. Phenotype-environment associations were also stronger in females than males, suggesting that natural selection due to abiotic conditions may act more strongly on females than males. Our results suggest that natural and sexual-selective pressures on phenotypic traits change during the process of habitat fragmentation, and that these changes are largely contingent upon existing habitat conditions within isolated fragments. Our study provides an improved understanding of the ecological and evolutionary consequences of habitat fragmentation and lends insight into the ability of some small populations to respond to selection and environmental change.

Territory size decreases minimally with increasing food abundance in stream salmonids: Implications for population regulation.

How the local density of territorial animals responds to changes in food abundance will depend on the flexibility of territory size. Quantitative estimates of territory size over a broad range of food abundance are relatively rare because of the difficulty of measuring food abundance in the wild. Stream salmonids are an ideal model system for investigating flexibility in territory size, because food abundance can be quantified in the field and manipulated in the laboratory. We conducted a meta-analysis to test whether territory size decreases with increasing food abundance, and a mixed model analysis to test among three competing predictions: with increasing food abundance, territory size will be (1) fixed-the slope of a regression of log territory size vs. log food abundance = 0; (2) flexible and decreasing, as if individuals are defending a fixed amount of food-a slope = -1; and (3) initially compressible, but with an asymptotic minimum size-a slope between 0 and -1. We collected data from 16 studies that manipulated or measured food abundance while monitoring changes in territory size of young-of-the-year salmonids; 10 were experimental laboratory studies, whereas six were observational field studies. Overall, territory size decreased significantly with increasing food abundance; the weighted average correlation coefficient was -0.31. However, the estimated slope of the relationship between log territory size and log food abundance was only -0.23, significantly different from 0, and also significantly shallower than -1. Our estimated slope suggests that attempts to increase the density of territorial salmonids by increasing food abundance and reducing territory size will be inefficient; a 20-fold increase in food abundance would be required to double population density. Our analysis may also have implications for other species with a territorial mosaic social system-i.e. contiguous territories. In these social systems, social inertia will dampen any effects of changes in food abundance on the local density of settlers, compared to non-territorial species or those with non-contiguous territories.

Sneaker Males Affect Fighter Male Body Size and Sexual Size Dimorphism in Salmon.

Large male body size is typically favored by directional sexual selection through competition for mates. However, alternative male life-history phenotypes, such as "sneakers," should decrease the strength of sexual selection acting on body size of large "fighter" males. We tested this prediction with salmon species; in southern populations, where sneakers are common, fighter males should be smaller than in northern populations, where sneakers are rare, leading to geographical clines in sexual size dimorphism (SSD). Consistent with our prediction, fighter male body size and SSD (fighter male∶female size) increase with latitude in species with sneaker males (Atlantic salmon Salmo salar and masu salmon Oncorhynchus masou) but not in species without sneakers (chum salmon Oncorhynchus keta and pink salmon Oncorhynchus gorbuscha). This is the first evidence that sneaker males affect SSD across populations and species, and it suggests that alternative male mating strategies may shape the evolution of body size.

Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling.

Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ~0.31%/MY (CI: 0.27-0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings represent an important contribution to the systematics of Salmonidae, and provide a useful tool for addressing questions related to fundamental and applied evolutionary issues.

The influence of operational sex ratio on the intensity of competition for mates.

The evolution and maintenance of secondary sexual characteristics and behavior are heavily influenced by the variance in mating success among individuals in a population. The operational sex ratio (OSR) is often used as a predictor of the intensity of competition for mates, as it describes the relative number of males and females who are ready to mate. We investigate changes in aggression, courtship, mate guarding, and sperm release as a function of changes in the OSR using meta-analytic techniques. As the OSR becomes increasingly biased, aggression increases as competitors attempt to defend mates, but this aggression begins to decrease at an OSR of 1.99, presumably due to the increased costs of competition as rivals become more numerous. Sperm release follows a similar but not significant trend. By contrast, courtship rate decreases as the OSR becomes increasingly biased, whereas mate guarding and copulation duration increase. Overall, predictable behavioral changes occur in response to OSR, although the nature of the change is dependent on the type of mating behavior. These results suggest considerable flexibility of mating system structure within species, which can be predicted by OSR and likely results in variation in the strength of sexual selection.

Courtship rate signals fertility in an externally fertilizing fish.

Sperm limitation is widespread across many animal species. Several mechanisms of sperm allocation have been proposed, including optimal allocation according to clutch size and equal allocation across females. However, considerably less effort has been directed at investigating the behavioural signals associated with sperm limitation in males, which may include mating rate and the intensity of courtship. We investigated whether multiple successive spawnings affect individual male fertilization success, mating rates and courtship rates in Japanese medaka (Oryzias latipes). Across an average of 17 spawning events per male, fertilization success decreased from 83.7 per cent for the first spawning to 40 per cent for the last spawning while courtship rate decreased from 3.4 to 1.5 min⁻¹. Females appeared to respond to male sperm depletion by reducing clutch size. Our results suggest that male Japanese medaka are sperm-limited, and that courtship rate may be an honest indication of fertilization ability.

Divergent compensatory growth responses within species: linked to contrasting migrations in salmon?

Animals often exhibit accelerated or "compensatory" growth (CG) after periods of environmentally induced growth depression, raising important questions about how they cope with environmental variability. We tested an underexplored hypothesis regarding the evolutionary consequences of CG; namely, that natural populations differ in CG responses. Common-garden experiments were used to compare subadult growth following food restriction between groups (control, treatment) of two Atlantic salmon (Salmo salar) populations and their first-generation (F(1)) hybrids. The populations are found at similar latitudes but characterized by differences in migration distance. We predicted that long-distance migrants would better maintain growth trajectories following food restriction than short-distance migrants because they: (1) require larger body sizes to offset energetic costs of migration and (2) face greater time constraints for growth as they must leave non-breeding areas earlier to return to breeding areas. Long-distance migrants grew faster, achieved quicker CG (relative to controls), and their overall body morphology was more streamlined (a trait known to improve swimming efficiency) than slower growing short-distance migrants. F(1) hybrids were generally intermediate in "normal" growth, CG, and body morphology. We concluded that CG responses may differ considerably among populations and that the conditions generating them are likely interconnected with selection on a suite of other traits.