Ingrid B. Spies

Genetic isolation by distance and localized fjord population structure in Pacific cod (Gadus macrocephalus): limited effective dispersal in the northeastern Pacific Ocean

Genetic population structure of Pacific cod, Gadus macrocephalus, was examined across much of its northeast- ern Pacific range by screening variation at 11 microsatellite DNA loci. Estimates of FST (0.005 ± 0.002) and RST (0.010 ± 0.003) over all samples suggested that effective dispersal is limited among populations. Genetic divergence was highly cor- related with geographic distance in an isolation-by-distance (IBD) pattern along the entire coastal continuum in the north- eastern Pacific Ocean (~4000 km; r 2 = 0.83), extending from Washington State to the Aleutian Islands, and over smaller geographic distances for three locations in Alaska (~1700 km; r 2 = 0.56). Slopes of IBD regressions suggested average dis- persal distance between birth and reproduction of less than 30 km. Exceptions to this pattern were found in samples taken from fjord environments in the Georgia Basin (the Strait of Georgia (Canada) and Puget Sound (USA)), where populations were differentiated from coastal cod. Our results showed population structure at spatial scales relevant to fisheries manage- ment, both caused by limited dispersal along the coast and by sharp barriers to migration isolating smaller stocks in coastal fjord environments.

Multiple ice‐age refugia in Pacific cod, Gadus macrocephalus

Pleistocene ice‐ages greatly influenced the historical abundances of Pacific cod, Gadus macrocephalus, in the North Pacific and its marginal seas. We surveyed genetic variation at 11 microsatellite loci and mitochondrial (mt) DNA in samples from twelve locations from the Sea of Japan to Washington State. Both microsatellite (mean H = 0.868) and mtDNA haplotype (mean h = 0.958) diversities were large and did not show any geographical trends. Genetic differentiation between samples was significantly correlated with geographical distance between samples for both microsatellites (FST = 0.028, r2 = 0.33) and mtDNA (FST = 0.027, r2 = 0.18). Both marker classes showed a strong genetic discontinuity between northwestern and northeastern Pacific populations that likely represents groups previously isolated during glaciations that are now in secondary contact. Significant differences appeared between samples from the Sea of Japan and Okhotsk Sea that may reflect ice‐age isolations in the northwest Pacific. In the northeast Pacific, a microsatellite and mtDNA partition was detected between coastal and Georgia Basin populations. The presence of two major coastal mtDNA lineages on either side of the Pacific Ocean basin implies at least two ice‐age refugia and separate postglacial population expansions facilitated by different glacial histories. Northward expansions into the Gulf of Alaska were possible 14–15 kyr ago, but deglaciation and colonization of the Georgia Basin probably occurred somewhat later. Population expansions were evident in mtDNA mismatch distributions and in Bayesian skyline plots of the three major lineages, but the start of expansions appeared to pre‐date the last glacial maximum.

Twelve microsatellite loci for lake trout (Salvelinus namaycush)

We describe 12 microsatellite loci isolated from lake trout (Salvelinus namaycush). The number of alleles at these loci ranged from two to 11 with an average of 5.3 alleles per locus. The expected heterozygosity ranged from 0.29 to 0.76, with an average of 0.68. Accidental (or illegal) introductions of lake trout into watersheds are decimating native trout populations in the northern Rocky Mountains, and these loci will be useful for identifying the source of these introductions and for estimating the number of founding individuals.

Genetic Assessment of the Mating System and Patterns of Egg Cannibalism in Atka Mackerel

Abstract The mating system and patterns of gender-specific egg cannibalism in Atka mackerel Pleurogrammus monopterygius were examined through genetic parentage analysis of embryos in egg clutches produced in captive and wild populations. Like other hexagrammid fishes, Atka mackerel exhibit polygynandry, which is characterized by serial matings by both genders within a breeding season. Most matings in captivity were pairings of females with nest-attendant males, although parentage analysis of clutches produced in a small tank with limited nesting substrate revealed that 31% contained contributions by non–nest-guarding males. In contrast, all egg clutches produced in a large exhibit tank were sired by guardian males. Multiple parentage, sometimes involving both genders, was detected in 35% of egg clutches collected in the field or retrieved from the guts of adult male and female cannibals. Half-sib and unrelated full-sib embryos were found in several putative clutches, indicating that the reproductive output from multiple males and females may be combined sequentially and fused into a single clutch. These results suggested that nest takeovers, combined with alloparental care of existing broods, represent common reproductive tactics in males. Egg cannibalism is a significant seasonal factor in the diets of male and female Atka mackerel. Analysis of loose eggs and partial egg clutches ingested by 4 female and 15 male cannibals showed that nearly all conspecific predation represented heterocannibalism. One instance of partial filial cannibalism was documented in a male that was one of multiple sires for the clutch.

Effects of Maternal Growth on Fecundity and Egg Quality of Wild and Captive Atka Mackerel

Abstract Trade-offs in energy allocation between growth and reproduction can result in variations in reproductive potential in fish with differing growth patterns. Spawning biomass is often used as a proxy for reproductive potential on the assumption that fecundity is directly proportional to body weight. We examined variations in the reproductive potential of Atka mackerel Pleurogrammus monopterygius by studying the effect of differential growth and condition patterns on fecundity, atresia, and egg energy. Fecundity and egg energy were determined for fish from two geographic areas, Seguam Pass and Amchitka Island, Alaska, and compared with those of fish held in captivity. These Atka mackerel showed distinct differences in growth and condition, with weight at length and length at age being the highest among captive fish, intermediate among fish from Seguam Pass, and lowest among fish from Amchitka Island. Realized fecundity showed that on average captive fish spawned seven batches, fish from Seguam Pass six batches, and fish from Amchitka Island five batches. For wild fish, potential and realized fecundity at length or age was significantly higher at Seguam Pass than at Amchitka Island, whereas the fecundity-at-weight relationship did not differ by area, suggesting that weight is a better predictor of fecundity than length or age. Atresia and batch fecundity by length or weight did not differ by area, suggesting that the variation in fecundity is better explained by the variation in batch number than by batch size. Oocyte dry weight was higher for captive fish than for wild fish, whereas batch order did not significantly affect oocyte dry weight. Increased potential fecundity, realized fecundity, and oocyte quality in Atka mackerel females were strongly related to body size, indicating that growth differences and maternal feeding success impact the fecundity and oocyte quality of Atka mackerel. Therefore, changes in growth and condition patterns need to be taken into account to accurately estimate the reproductive potential of this species.

Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod

Significance Estimates of migration are important for understanding the dynamics of natural populations. A statistic known as FST is often used to measure levels of genetic differentiation among natural populations. Equations that translate FST into estimates of migration are based on “ideal” populations, which are subject to many simplifying assumptions compared with real populations. Therefore, theoretical estimates of migration might not be realistic. We modeled populations of Atlantic cod in the North Sea and the adjacent Skagerrak region to compare how migration is related to the complexities of real populations, and how actual migration compares with predictions based on theory. Results are intended to help apply population genetic theory to practical situations. Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator FST, such as Wright’s equation, FST ≈ 1/(4Nem + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the Ne/Nt ratio (where Ne is the effective and Nt is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased Ne/Nt and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of FST, particularly when genetic differentiation was low, FST ≈ 10−3. Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations.