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Data from: Does human-induced hybridization have long-term genetic effects? Empirical testing with domesticated, wild and hybridized fish populations
Harbicht, Andrew; Wilson, Chris C.; Fraser, Dylan J. — 2014-07-25 Current conservation practices exclude human-generated hybridized populations from protection, as the genetic effects of hybridization in the wild have been observed to be long-lasting based on neutral genetic markers and are considered potentially irreversible. Theory, however, predicts otherwise for genes under selection. We transplanted combinations of wild, domesticated and hybridized populations of a fish species to new environments. We then compared survival, phenotypic variation and plasticity to determine whether hybridization affects adaptive potential after multiple generations of selection in the wild. Although the fitness of our hybridized populations at the onset of hybridization cannot be assessed, our results suggest that within five to eleven generations, selection can remove introduced foreign genes from wild populations that have hybridized with domesticated conspecifics. The end result is hybridized populations that, in terms of survival, phenotypic plasticity, mean trait expression and overall general responses to environmental change, closely resemble neighbouring wild populations. These results have important implications for considering the potential conservation value of hybridized populations and illustrate the effectiveness of selection in a local environment.
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Data from: Are heritability and selection related to population size in nature? Meta-analysis and conservation implications
Wood, Jacquelyn L.A.; Yates, Matthew C.; Fraser, Dylan J.; Wood, Jacquelyn L. A. — 2016-03-03 It is widely thought that small populations should have less additive genetic variance and respond less efficiently to natural selection than large populations. Across taxa, we meta-analytically quantified the relationship between adult census population size (N) and additive genetic variance (proxy: h2) and found no reduction in h2 with decreasing N; surveyed populations ranged from four to one million individuals (1735 h2estimates, 146 populations, 83 species). In terms of adaptation, ecological conditions may systematically differ between populations of varying N; the magnitude of selection these populations experience may therefore also differ. We thus also meta-analytically tested whether selection changes with N, and found little evidence for systematic differences in the strength, direction, or form of selection with N across different trait types and taxa (7344 selection estimates, 172 populations, 80 species). Collectively, our results (i) indirectly suggest that genetic drift neither overwhelms selection more in small than in large natural populations, nor weakens adaptive potential/h2 in small populations, and (ii) imply that natural populations of varying sizes experience a variety of environmental conditions, without consistently differing habitat quality at small N. However, we caution that the data are currently insufficient to determine whether some small populations may retain adaptive potential definitively. Further study is required into (i) selection and genetic variation in completely isolated populations of known N, underrepresented taxonomic groups, and non-generalist species, (ii) adaptive potential using multidimensional approaches, and (iii) the nature of selective pressures for specific traits. https://creativecommons.org/publicdomain/zero/1.0/
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Data from: Does source population size affect performance in new environments?
Yates, Matthew C.; Fraser, Dylan J. — 2014-05-27 Small populations are predicted to perform poorly relative to large populations when experiencing environmental change. To explore this prediction in nature, data from reciprocal transplant, common garden, and translocation studies were compared meta-analytically. We contrasted changes in performance resulting from transplantation to new environments among individuals originating from different sized source populations from plants and salmonids. We then evaluated the effect of source population size on performance in natural common garden environments and the relationship between population size and habitat quality. In ‘home-away’ contrasts, large populations exhibited reduced performance in new environments. In common gardens, the effect of source population size on performance was inconsistent across life-history stages (LHS) and environments. When transplanted to the same set of new environments, small populations either performed equally well or better than large populations, depending on life stage. Conversely, large populations outperformed small populations within native environments, but only at later life stages. Population size was not associated with habitat quality. Several factors might explain the negative association between source population size and performance in new environments: (i) stronger local adaptation in large populations and antagonistic pleiotropy, (ii) the maintenance of genetic variation in small populations, and (iii) potential environmental differences between large and small populations.
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Data from: A critical assessment of estimating census population size from genetic population size (or vice versa) in three fishes
Yates, Matthew Carl; Bernos, Thais A.; Fraser, Dylan J. — 2017-05-26 Technological and methodological advances have facilitated the use of genetic data to infer census population size (Nc) in natural populations, particularly where traditional mark-and-recapture is challenging. The effective number of breeders (Nb) describes how many adults effectively contribute to a cohort and is often correlated with Nc. Predicting Nc from Nb or vice-versa in species with overlapping generations has important implications for conservation by permitting (i) estimation of the more difficult to quantify variable and (ii) inferences of Nb/Nc relationships in related species lacking data. We quantitatively synthesized Nb/Nc relationships in three salmonid fishes where sufficient data has recently accumulated. Mixed-effects models were analyzed in which each variable was included as a dependent variable or predictor term (Nb from Nc and vice versa). Species-dependent Nb/Nc slope estimates were significantly positive in two of three species; variation in species slopes were likely due to varying life histories and reinforce caution when inferring Nb/Nc from taxonomically-related species. Models provided maximum probable estimates for Nb and Nc for two species. However, study, population, and year effects explained substantial amounts of variation (39-57%). Consequently, prediction intervals were wide and included or were close to zero for all population sizes and species; model predictive utility was limited. Cost-benefit trade-offs when estimating Nb and/or Nc were also discussed using a real-world system example. Our findings based on salmonids suggest that no short-cuts currently exist when estimating population size; researchers should focus on quantifying the variable of interest or be aware of caveats when inferring the desired variable because of cost or logistics. We caution that the salmonid species examined share life-history traits that may obscure relationships between Nb and Nc. Sufficient data on other taxa were unavailable; additional research examining Nb/Nc relationships in species with potentially relevant life-history trait differences (e.g. differing survival curves) are needed.
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Data from: Spatiotemporal relationship between adult census size and genetic population size across a wide population size gradient
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Bernos, Thaïs A.; Fraser, Dylan J. — 2016-08-01 Adult census population size (N) and effective number of breeders (Nb) are highly relevant for designing effective conservation strategies. Both parameters are often challenging to quantify, however, making it of interest to determine whether one parameter can be generalized from the other. Yet, the spatiotemporal relationship between N and Nb has not been well characterized empirically in many taxa. We analysed this relationship for 5–7 consecutive years in twelve brook trout populations varying greatly in N (49-10032) and Nb (3-567) and identified major environmental variables affecting the two parameters. N or habitat size alone explained 47–57% of the variance in Nb, and Nb was strongly correlated with effective population size. The ratio Nb/N ranged from 0.01 to 0.45 and increased at small N or following an annual decrease in N, suggesting density-dependent constraints on Nb. We found no evidence for a consistent, directional difference between variability in Nb and/or Nb/N among small and large populations; however, small populations had more varying temporal variability in Nb/N ratios than large populations. Finally, Nb and Nb/N were 2.5- and 2.3-fold more variable among populations than temporally within populations. Our results demonstrate a clear linkage between demographic and evolutionary parameters, suggesting that Nb could be used to approximate N (or vice versa) in natural populations. Nevertheless, using one variable to infer the other to monitor trends within populations is less recommended, perhaps even less so in small populations given their less predictable Nb vs. N dynamics.
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Data from: Multigenerational hybridisation and its consequences for maternal effects in Atlantic salmon
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Debes, Paul V.; McBride, Meghan C.; Fraser, Dylan J.; Hutchings, Jeffrey A. — 2013-04-01 Outbreeding between segregating populations can be important from an evolutionary, conservation, and economical- agricultural perspective. Whether and how outbreeding influences maternal effects in wild populations has rarely been studied, despite both the prominent maternal influence on early offspring survival and the known presence of fitness effects resulting from outbreeding in many taxa. We studied several traits during the yolk-feeding stage in multigenerational crosses between a wild and a domesticated Atlantic salmon (Salmo salar) population up to their third-generation hybrid in a common laboratory environment. Using cross-means analysis, we inferred that maternal additive outbreeding effects underlie most offspring traits, but that yolk mass also underlies maternal dominant effects. As a consequence of the interplay between additive and dominant maternally controlled traits, offspring from first-generation hybrid mothers expressed an excessive proportion of residual yolk mass, relative to total mass, at time of first feeding. Their residual yolk mass was 23-97% greater than those of other crosses and 31% more than that predicted by a purely additive model. Offspring additive, epistatic, and epistatic offspring-by-maternal outbreeding effects appeared to further modify this largely maternally controlled cross-means pattern, resulting in an increase in offspring size with the percentage of domesticated alleles. Fitness implications remain elusive because of unknown phenotype- by-environment interactions. However, these results suggest how mechanistically co-adapted genetic maternal control on early offspring development can be disrupted by the effects of combining alleles from divergent populations. Complex outbreeding effects at both the maternal and offspring levels make the prediction of hybrid phenotypes difficult.
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Data from: Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish
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Fraser, Dylan J.; Debes, Paul V.; Bernatchez, Louis; Hutchings, Jeffrey A. — 2014-07-03 Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest.
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Rocky Mountain alpine lake brook trout census and effective sizes [2017-2019]
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Clarke, Shannon H.; McCracken, Gregory R.; Humphries, Shelley; Ruzzante, Daniel E.; Grant, James W.A.; Fraser, Dylan J. — 2022-04-20 Data were collected each year during the summer from 2017 to 2019. Census size (Nc) estimates were generated using mark-recapture methods involving multiple recapture events, and estimated using the Schnabel method. Effective number of breeder (Nb) estimates were generated using the Linkage Disequilibrium Method in the NeEstimator V2 software, from genotypes of year 0+ individuals. Three of these lakes were subjected to size-selective harvesting beginning in the fall of 2017, and were harvested each proceeding fall.
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Data from: Novel, continuous monitoring of fine-scale movement using fixed-position radiotelemetry arrays and random forest location fingerprinting
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Harbicht, Andrew B.; Castro-Santos, Theodore; Ardren, William R.; Gorsky, Dimitry; Fraser, Dylan J. — 2018-01-19 1. Radio-tag signals from fixed-position antennas are most often used to indicate presence/absence of individuals, or to estimate individual activity levels from signal strength variation within an antenna’s detection zone. The potential of such systems to provide more precise information on tag location and movement has not been explored in great detail in an ecological setting. 2. By reversing the roles that transmitters and receivers play in localization methods common to the telecommunications industry, we present a new telemetric tool for accurately estimating the location of tagged individuals from received signal strength values. The methods used to characterize the study area in terms of received signal strength are described, as is the random forest model used for localization. The resulting method is then validated using test data before being applied to true data collected from tagged individuals in the study site. 3. Application of the localization method to test data withheld from the learning dataset indicated a low average error over the entire study area (< 1m) while application of the localization method to real data produced highly probable results consistent with field observations. 4. This telemetric approach provided detailed movement data for tagged fish along a single axis (a migratory path) and is particularly useful for monitoring passage along migratory routes. The new methods applied in this study can also be expanded to include multiple axes (x, y, z) and multiple environments (aquatic and terrestrial) for remotely monitoring wildlife movement.
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Data from: Striking phenotypic variation yet low genetic differentiation in sympatric lake trout (Salvelinus namaycush)
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Marin, Kia; Coon, Andrew; Carson, Robert; Debes, Paul V.; Fraser, Dylan J. — 2017-08-26 The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists.

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(Author: Fraser, Dylan J.)

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