Christopher T. Taggart

A nuclear DNA basis for shelf‐ and bank‐scale population structure in northwest Atlantic cod (Gadus morhua): Labrador to Georges Bank

Variation at five microsatellite DNA loci scored in ≈ 1300 individuals provided evidence of genetic structure among 14 cod (Gadus morhua) populations spanning the range of the species in the northwest (NW) Atlantic. Using DA and DSW measures of genetic distance, as well as FST and RST measures of population structure, differences are revealed among populations at continental shelf scales (NE Newfoundland Shelf, Grand Banks, Flemish Cap, Scotian Shelf, Georges Bank) where regions are separated by submarine saddles, channels and trenches. However, we also provide evidence of genetic structure at spawning‐bank scales consistent with variation in oceanographic features and in the spatiotemporal distribution of spawning, each of which may represent barriers to gene flow among geographically contiguous populations inhabiting a highly advective environment. The differences described are consistent with postdispersal spawning fidelity to natal areas, a behaviour that may be facilitated by topographically induced gyre‐like circulations that can act as retention mechanisms. Significant degrees of substructure among neighbouring and contiguous cod populations may be most easily explained by the associated oceanographic features and processes that conceivably form the template for the evolution of the structure. We suggest that bathymetric and hydrodynamic structure represents a rational starting point for developing hypotheses to examine the processes that lead to the genetic structuring of marine fish species.

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n = 40) for which allele frequencies show parallel temperature-associated clines (p < 0.001, r2 = 0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted ‘neutral’ loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.

Stability in the historical pattern of genetic structure of Newfoundland cod (Gadus morhua) despite the catastrophic decline in population size from 1964 to 1994

We report on evidence of long term stability inthe geographic pattern of geneticdifferentiation among cod (Gadus morhua)collected from 5 spawning banks offNewfoundland and Labrador over a periodspanning three decades (1964–1994) and 2orders of magnitude of population sizevariation. Six microsatellite DNA lociamplified from archived otoliths (1964 and1978) and contemporary (1990s) tissue samplesrevealed fidelity to natal spawning banks overthis period. A two level (spawning bank anddecade) hierarchical and multilocus AMOVAindicated that 1.55% of the total variation inallele frequencies could be attributed(P = 0.036) to spatial structure while novariance component could be attributed totemporal changes. A finer scale analysis amongcod from just 3 of these spawning banksreveals, however, evidence consistent with somepost-collapse mixing between cod from twobanks. In the context of fisheries managementand conservation, the survival of the spatialpattern of genetic differentiation during thepopulation collapse suggests that if recoveryeventually occurs it will likely be throughpopulation re-growth in situ rather thanby migratory influx.

A review of the evidence for genetic structure of cod (Gadus morhua) populations in the NW Atlantic and population affinities of larval cod off Newfoundland and the Gulf of St. Lawrence

Abstract We review our recent studies on the genetic structure of Atlantic cod (Gadus morhua) populations in the NW Atlantic. Our conclusions are based on knowledge of polymorphism at microsatellite DNA loci combined with known aspects of cod biology and ecology and with known oceanographic features in the NW Atlantic. Three case studies illustrate genetic heterogeneity between cod populations at the meso- and large-scales of coastal embayments and offshore banks and at the small-scale of oceanographic features. Our results generally highlight the importance of combining genetic with physiological, ecological, and oceanographic information, when assessing the genetic structure of highly abundant, widely distributed, and high gene-flow marine fish species. We highlight the role that oceanographic features (e.g., gyre-like systems) and known spatio-temporal differences in spawning time may play as barriers to gene-flow between and among neighboring and often contiguous cod populations in the NW Atlantic. We suggest that bathymetric and hydrodynamic/oceanographic structure represents a rational starting point for developing hypotheses aimed at assessing the genetic structure of high gene-flow marine fish species.

Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish

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.

MIXED‐STOCK ANALYSIS OF ATLANTIC COD NEAR THE GULF OF ST. LAWRENCE BASED ON MICROSATELLITE DNA

The collapse of various stock complexes of cod (Gadus morhua) in the northwest Atlantic has prompted a clarification of relationships among stock components. Here we examine the genetic composition of >2300 cod collected during 1994-1997 in the Gulf of St. Lawrence and its approaches to determine whether: (1) stock components can be genetically identified; (2) population structure is temporally stable; (3) components are always separated and, if not, where and when are they mixed; and (4) component contributions to mixtures can be estimated. We use polymorphism at six microsatellite DNA loci from cod collected on or near their spring and summer spawning grounds to examine structure and then employ maximum likelihood analyses to estimate contributions of each component to mixtures overwintering near the entrance to the Gulf. Estimates of genetic structure (FST and RST) reveal significant differences among cod populations during stock- separated periods, and the structure appears to be temporally stable. Multidimensional scaling analysis of estimates of genetic distance (DA) suggest that the structure results from differences among cod collected within the Gulf of St. Lawrence and those collected near the entrance to the Gulf on either side of the Laurentian Channel in the Cabot Strait, as well as among cod collected south of Newfoundland along the north side of the Channel. Weak genetic heterogeneity among seven regional mixed-stock collections during the over- wintering period suggests that cod aggregations characteristically found in the overwintering region represent population mixtures that differ in the proportion of cod contributed to them by the various stock components. Maximum likelihood estimates indicate no signif- icant temporal changes in component contributions to the mixed-stock samples between 1996 and 1997. when all of the winter mixed-stock samples were pooled. The combined contribution of cod from the southern and northern Gulf of St. Lawrence to the. mixed- stock samples ranged between 46% and 71% (expected 64%). More precise estimates of contributions from these two regions are precluded by the weak genetic differentiation detected in our samples. The contribution by cod from the Cape Breton Island region was small and estimated at 3%. Contributions by cod from the eastern Scotian Shelf, southwest Newfoundland and south-central Newfoundland were in the range of 13-14%, 4%, and 8%, respectively. Contributions by inshore cod from Placentia and Fortune Bays in south Newfoundland were small to negligible (-3% each). The results indicate that future man- agement could be designed around the spatial and temporal scale of the stock structure identified during the stock-separated period and around the spatially varying contributions to the overwintering mixed-stock fishery.

Accelerometer tags: detecting and identifying activities in fish and the effect of sampling frequency

SUMMARY Monitoring and measuring the behaviour and movement of aquatic animals in the wild is typically challenging, though micro-accelerometer (archival or telemetry) tags now provide the means to remotely identify and quantify behavioural states and rates such as resting, swimming and migrating, and to estimate activity and energy budgets. Most studies use low-frequency (≤32 Hz) accelerometer sampling because of battery and data-archiving constraints. In this study we assessed the effect of sampling frequency (aliasing) on activity detection probability using the great sculpin (Myoxocephalus polyacanthoceaphalus) as a model species. Feeding strikes and escape responses (fast-start activities) and spontaneous movements among seven different great sculpin were triggered, observed and recorded using video records and a tri-axial accelerometer sampling at 100 Hz. We demonstrate that multiple parameters in the time and probability domains can statistically differentiate between activities with high detection (90%) and identification (80%) probabilities. Detection probability for feeding and escape activities decreased by 50% when sampling at <10 Hz. Our analyses illustrate additional problems associated with aliasing and how activity and energy-budget estimates can be compromised and misinterpreted. We recommend that high-frequency (>30 Hz) accelerometer sampling be used in similar laboratory and field studies. If battery and/or data storage is limited, we also recommend archiving the events via an on-board algorithm that determines the highest likelihood and subsequent archiving of the various event classes of interest.

Genetic Differentiation, Temporal Stability, and the Absence of Isolation by Distance among Atlantic Herring Populations

Abstract The genetic variation among 17 spawning groups of Atlantic herring Clupea harengus was assessed at several temporal and spatial scales using nine tetranucleotide microsatellites. Pan-Atlantic samples were drawn from the Scotian Shelf, the Celtic Sea, the Baltic Sea, and coastal Iceland. Significant differentiation was observed between northeastern and northwestern Atlantic herring (F ST ∼ 0.065) and among northwestern Atlantic spawning groups (max F ST = 0.014) at the spatial scale of the Scotian Shelf. Geographic distance among Scotian Shelf collections did not explain the pattern of genetic differentiation observed (e.g., lack of isolation by distance). The temporal proximity of collections (as measured by days between collections) explained 30% of the pairwise population differentiation (P = 0.0025). Allele frequencies of replicate samples and year-class analyses demonstrate temporal stability at four locations.

Can changes in length-at-age and maturation timing in Scotian Shelf haddock (Melanogrammus aeglefinus) be explained by fishing?

Factors affecting size-at-age in fish populations include temperature and fishing where the latter can represent a strong selective force on size-at-age variation through changes in population growth and maturation. Over the past three decades, Scotian Shelf haddock (Melanogrammus aeglefinus) exhibited declines in maturation timing and mature fish length-at-age. Here, we examine these declines with respect to temperature, stock biomass, and fishing. We employ the thermal integral (growing degree-day, GDD, 8Cday) to examine the variation in length-at-age (length-at-day, LaD, cm) and maturity (age-at-50%-maturity) that is attributable to temperature. Unexplained variation in LaD and age-at-50%-ma- turity remains and is characterized by declines in the LaD-at-GDD regression parameters and the thermal constant for ma- turity with increasing year-class. We find no significant correlation between the temperature-independent declines in LaD and stock biomass. The combination of high fishing mortality (favouring early maturation) and sustained harvesting of large fish (fast-growing, late-maturing individuals) offers the simplest explanation for the systematic decline in inferred growth and age-at-maturity for Scotian Shelf haddock. These results are consistent with other exploited populations and re- cent laboratory experiments quantifying the effects of fishing on size-at-age and age-at-maturity.

Characterization of North Atlantic right-whale (Eubalaena glacialis) sounds in the Bay of Fundy

Hydrophone recordings, made in the presence of North Atlantic right whales (Eubalaena glacialis) in the Bay of Fundy during the daytime in July 1999, are used to determine the characteristics of the recorded sounds. A spectrogram-based method was implemented to discriminate whale sounds from background noise and the time-frequency envelope of the primary harmonic in the spectrogram was used as the basis for sound characterization. Sounds were typically (82%, n=45) in the 300- to 600-Hz range with up- and downsweeping modulations. Lower ( 900 Hz) frequency sounds were relatively rare. Most sounds were frequency modulated, with 95% of the observed instantaneous relative frequency variation being within /spl plusmn/4.5% of the mean peak frequency. Harmonics were observed in 18% of the sounds. The average sound duration was 0.42 s/spl plusmn/0.26 SD. The sounds occurred at a rate of between 0.3 and 0.7 min/sup -1/. The time intervals between adjacent sounds (2-700 s) were not randomly distributed. The number of sounds occurring among different waiting times did not reflect a Poisson distribution and a clustering of sounds (2 to 5 cluster/sup -1/) was observed. The sound characteristics are compared to those documented elsewhere and as reported for the southern right whale.