Bentzen, Paul

Permanent URI for this collectionhttps://hdl.handle.net/10222/22289

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Open Access
Both Geography and Ecology Contribute to Mating Isolation in Guppies
(2010-12) Schwartz, Amy K.; Weese, Dylan J.; Bentzen, Paul; Kinnison, Michael T.; Hendry, Andrew P.
Local adaptation to different environments can promote mating isolation - either as an incidental by-product of trait divergence, or as a result of selection to avoid maladaptive mating. Numerous recent empirical examples point to the common influence of divergent natural selection on speciation based largely on evidence of strong pre-mating isolation between populations from different habitat types. Accumulating evidence for natural selection's influence on speciation is therefore no longer a challenge. The difficulty, rather, is in determining the mechanisms involved in the progress of adaptive divergence to speciation once barriers to gene flow are already present. Here, we present results of both laboratory and field experiments with Trinidadian guppies (Poecilia reticulata) from different environments, who do not show complete reproductive isolation despite adaptive divergence. We investigate patterns of mating isolation between populations that do and do not exchange migrants and show evidence for both by-product and reinforcement mechanisms depending on female ecology. Specifically, low-predation females discriminate against all high-predation males thus implying a by-product mechanism, whereas high-predation females only discriminate against low-predation males from further upstream in the same river, implying selection to avoid maladaptive mating. Our study thus confirms that mechanisms of adaptive speciation are not necessarily mutually exclusive and uncovers the complex ecology-geography interactions that underlie the evolution of mating isolation in nature.
Open Access
Identifying Canadian Freshwater Fishes through DNA Barcodes
(2008-06) Hubert, Nicolas; Hanner, Robert; Holm, Erling; Mandrak, Nicholas E.; Taylor, Eric; Burridge, Mary; Watkinson, Douglas; Dumont, Pierre; Curry, Allen; Bentzen, Paul; Zhang, Junbin; April, Julien; Bernatchez, Louis
Background: DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 59 region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings: We bi-directionally sequenced the standard 652 bp "barcode'' region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance: The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.
Open Access
Population Structure as Revealed by mtDNA and Microsatellites in Northern Fur Seals, Callorhinus ursinus, throughout Their Range
(2010-05) Dickerson, Bobette R.; Ream, Rolf R.; Vignieri, Sacha N.; Bentzen, Paul
Background: The northern fur seal (Callorhinus ursinus; NFS) is a widely distributed pinniped that has been shown to exhibit a high degree of philopatry to islands, breeding areas on an island, and even to specific segments of breeding areas. This level of philopatry could conceivably lead to highly genetically divergent populations. However, northern fur seals have the potential for dispersal across large distances and have experienced repeated rapid population expansions following glacial retreat and the more recent cessation of intensive harvest pressure. Methodology/Principal Findings: Using microsatellite and mitochondrial loci, we examined population structure in NFS throughout their range. We found only weak population genetic structure among breeding islands including significant F(ST) and Phi(ST) values between eastern and western Pacific islands. Conclusions: We conclude that insufficient time since rapid population expansion events (both post glacial and following the cessation of intense harvest pressure) mixed with low levels of contemporary migration have resulted in an absence of genetic structure across the entire northern fur seal range.
Open Access
Mixed evidence for reduced local adaptation in wild salmon resulting from interbreeding with escaped farmed salmon: complexities in hybrid fitness
(2008-08) Fraser, Dylan J.; Cook, Adam M.; Eddington, James D.; Bentzen, Paul; Hutchings, Jeffrey A.
Interbreeding between artificially-selected and wild organisms can have negative fitness consequences for the latter. In the Northwest Atlantic, farmed Atlantic salmon recurrently escape into the wild and enter rivers where small, declining populations of wild salmon breed. Most farmed salmon in the region derive from an ancestral source population that occupies a nonacidified river (pH 6.0-6.5). Yet many wild populations with which escaped farmed salmon might interbreed inhabit acidified rivers (pH 4.6-5.2). Using common garden experimentation, and examining two early-life history stages across two generations of interbreeding, we showed that wild salmon populations inhabiting acidified rivers had higher survival at acidified pH than farmed salmon or F(1) farmed-wild hybrids. In contrast, however, there was limited evidence for reduced performance in backcrosses, and F(2) farmed-wild hybrids performed better or equally well to wild salmon. Wild salmon also survived or grew better at nonacidified than acidified pH, and wild and farmed salmon survived equally well at nonacidified pH. Thus, for acid tolerance and the stages examined, we found some evidence both for and against the theory that repeated farmed-wild interbreeding may reduce adaptive genetic variation in the wild and thereby negatively affect the persistence of depleted wild populations.
Open Access
Synchronized hatch and its ecological significance in rainbow smelt Osmerus mordax in St. Mary's Bay, Newfoundland
(2004-11) Bradbury, IR; Campana, SE; Bentzen, Paul; Snelgrove, PVR
Early life history stages in most marine animals are subject to high mortality through predation, starvation, and dispersal. Accordingly, the potential exists for the selection of behavioral mechanisms that reduce mortality. We examined the ecological significance of synchronization in hatch and the initiation of larval drift in rainbow smelt, Osmerus mordax, populations in St. Mary's Bay, Newfoundland. Larval abundances from six 24-h ring net surveys (2-h intervals) in Colinet and Salmonier Rivers during 2002/2003 suggest synchronized hatch following dusk (similar to2200 h). Monitoring of egg hatching in situ confirmed synchrony was at hatch and not emergence. Larval abundance showed no relationship with temperature or flow rates, and the consistency in hatch pattern suggested a light/dark cue. In experimental manipulations in which eggs were exposed to light and dark conditions for 2-h periods, hatch percentages were up to five times higher (p < 0.005) in dark treatments. We hypothesized that the linkage of hatch to low light levels represents a mechanism to avoid elevated larval predation in daylight conditions. Egg predation determined from predator gut content analysis suggested that extreme predation risk from small (< 20 cm) salmonids peaked during the day, prior to dusk, and was lowest during night (2200-0400 h). Microcosm experiments demonstrated that newly hatched larvae exposed to predators in dark conditions did not change in number, but mortality averaged 60% in light conditions. Our results suggest that predation pressure during the early life history of aquatic organisms might play a strong role in the optimization of aquatic life histories.
Open Access
Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish
(2013-04) Bradbury, Ian R.; Hubert, Sophie; Higgins, Brent; Bowman, Sharen; Borza, Tudor; Paterson, Ian G.; Snelgrove, Paul V. R.; Morris, Corey J.; Gregory, Robert S.; Hardie, David; Hutchings, Jeffrey A.; Ruzzante, Daniel E.; Taggart, Christopher T.; Bentzen, Paul
As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.
Open Access
Non-linear genetic isolation by distance: implications for dispersal estimation in anadromous and marine fish populations
(2007) Bradbury, Ian R.; Bentzen, Paul
Indirect genetic approaches such as those based on the association between genetic and geographic distance (isolation by distance, IBD) may provide one of the best means of estimating dispersal in marine systems. We evaluated the scale -dependency and the ecological covariates of the 1131) relationship through a combined modeling and meta-analytical approach. Using Wright's fixation index F-ST, simulations were used to generate IBD relationships, F-ST/(1-F-ST) and geographic distance, for various combinations of average dispersal distance and number of generations. 1131) linearity increased with time since colonization and dispersal distance, although the effect of dispersal distance predominated after initial colonization. Simulations suggest that declines in the 1131) slope were associated with increases in the spatial scale of observation, suggesting that the IBD pattern is non-linear at very short and long average dispersal distances. We hypothesized that non-linear IBD would be common in marine populations, and apparent through a biologically significant non-zero intercept arid decreasing slope with increasing geographic scale. Predictions of common non-linearity were examined through IBD relationships (i.e. slope, intercept, R-2 of the regression) and life history parameters from the published literature for 18 species of anadromous/philopatric fishes. As predicted, 1131) parameters (intercept and slope) were consistently correlated with many life history traits (e.g. fecundity, egg size). However, the statistical removal of adult size eliminated most significant life history-IBD, correlations. Increases in IBD slope were associated with decreasing gene flow (p = 0.014, R-2 = 0.33), and decreasing migration distance (p = 0.039, R-2 = 0.23). Non-linearity was further supported by consistent declines in the 1131) slope with increased geographic scale in anadromous fish as well as several marine species, suggesting the ubiquity of this phenomenon. We conclude that isolation by distance patterns may reflect dispersal phenotype and are biologically significant. Nonetheless, non-linearity in 1131) pattern is probably the norm in aquatic organisms, resulting from large ranges and limited dispersal. Accordingly, approximations of demographic parameters based on the IBD must be made cautiously, taking into account possible non-linearity, scale dependencies, and assumptions of genetic drift-dispersal equilibrium.
Open Access
Otolith elemental composition and adult tagging reveal spawning site fidelity and estuarine dependency in rainbow smelt
(2008) Bradbury, I. R.; Campana, S. E.; Bentzen, Paul
Observations of homing and straying in marine organisms based on traditional Eulerian approaches may fail to resolve dispersal kernels or be unable to differentiate homing from invariant local residency, The roles of spawning site fidelity and straying in structuring populations of anadromous smelt Osmerus mordax were examined in coastal Newfoundland through the analysis of otolith elemental composition and a series of adult tagging experiments. Otolith elemental baselines were generated from freshwater residents, estuarine juveniles and laboratory-held individuals (32 psu), using both a single-element (i.e, Sr:Ca and Ba:Ca) and multivariate approach (i.e. discriminant function analysis). Ten spawning fish Of unknown dispersal history were sampled from each of 6 spawning locations, and otolith composition was examined using laser ablation inductively coupled plasma mass spectrometry at 12 to 16 locations across each otolith. Single-element and multivariate approaches both indicated estuarine residency predominated, with limited marine (0.7 %) signatures indicative of rare marine movements, Multiyear spawning site fidelity was examined through a finclipping (2003, n = 7076) and visual implant elastomer (VIE) experiment (2004, n = 13 524), encompassing each of the 6 spawning locations. We observed limited straying, with 90 to 99%, annual spawning site fidelity. Tag returns declined significantly with distance from location of tagging, and declines were linear over small (<50 km) distances (VIE: 1) < 0.001, r(2) = 0.99; fin clipping: 1) < 0.001, r(2) = 0.56). We conclude that population structure in anadromous smelt is maintained by small-scale habitat associations limited to a single estuary, supporting a hypothesis of demographic isolation among estuaries.
Open Access
Contemporary nuclear and mitochondrial genetic clines in a north temperate estuarine fish reflect Pleistocene vicariance
(2011) Bradbury, I. R.; Coulson, M. W.; Campana, S. E.; Paterson, I. G.; Bentzen, Paul
Contemporary genetic spatial structure in north temperate marine species is likely the culmination of multiple vicariant and dispersive cycles. Here we evaluate spatial genetic structure in an estuarine fish, rainbow smelt Osmerus mordax, from coastal Newfoundland, Canada, using data from both mtDNA (ND5) sequences and nuclear loci (11 microsatellites). Sequence analysis of ND5 identified a previously unrecognized genetic discontinuity between 2 hypo thesized glacial clades in southeastern Newfoundland. Microsatellite based tests for directional selection identified a locus (Omo11, p < 0.001) that mirrored mtDNA clades in the geographic distribution of its 2 common alleles but did not display elevated differentiation following correction for heterozygosity. Bayesian multilocus clustering of the remaining micro satellite loci supported the presence of 2 predominant groups, for which the spatial distribution was also largely consistent with those of the mtDNA and Omo11 clades. Taken together, the similarity in microsatellite and mtDNA clines supports the hypothesis that contemporary spatial structure in smelt reflects historical landscape isolation maintained by low dispersal and selective processes producing reinforcement between diverging populations. As genetic structure in northern marine and estuarine species may be largely determined by historical glacial cycles of vicariance, contemporary estimates of connectivity should be interpreted in the context of both past and present landscape structure.
Open Access
Microsatellite and allozyme analyses reveal few genetic differences among spatially distinct aggregations of geoduck clams (Panopea abrupta, Conrad 1849)
(2004-12) Vadopalas, B.; Leclair, LL; Bentzen, Paul
The genetic population structure of geoduck clams (Panopea abrupta) in inland waters of Washington may affect fishery management and aquacultural practices involving this species. To investigate genetic differentiation in geoduck clams, samples were collected from 16 Washington State sites located in the five Puget Sound sub basins, southern Georgia Strait, and the Strait of Juan de Fuca. A collection from Clarence Strait in SE Alaska was included as an outgroup. Individuals were genotyped at 11 allozyme and 7 microsatellite loci. There was little differentiation overall, but the Freshwater Bay collection in the Strait of Juan de Fuca was differentiated from others at both microsatellite and allozyme loci. For both marker classes, there was no evidence of significant correlation between genetic and geographic distance measures. In contrast to the microsatellite loci, the allozyme loci were in Hardy-Weinberg Equilibrium (HWE). Deviations from HWE expectations at microsatellite loci were interpreted as being primarily due to primer-site sequence variation rather than population level processes such as inbreeding.

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