W. Stewart Grant

Limits of Bayesian skyline plot analysis of mtDNA sequences to infer historical demographies in Pacific herring (and other species)

A previous analysis of Pacific herring mitochondrial (mt) DNA with Bayesian skyline plots (BSPs) was interpreted to reflect population growth in the late Pleistocene that was preceded by population stability over several hundred thousand years. Here we use an independent set of mtDNA control region (CR) sequences and simulations to test these hypotheses. The CR haplotype genealogy shows three deeply divided lineages, A, B and C, with divergences ranging from d=1.6% to 1.9% and with similar genetic diversities (h=0.95, 0.96, 0.94; Θ(π)=0.011, 0.012, 0.014, respectively). Lineage A occurs almost exclusively in the NW Pacific and Bering Sea, but lineages B and C are co-distributed in the Northeastern Pacific. This distribution points to a historical allopatric separation between A and B-C across the North Pacific during Pleistocene glaciations. The origins of B and C are uncertain. One hypothesis invokes long-term isolation of lineage C in the Sea of Cortez, but the present-day lack of geographical segregation from lineage B argues for lineage sorting to explain the deep divergence between B and C. BSPs depict rapid population growth in each lineage, but the timing of this growth is uncertain, because of questions about an appropriate molecular clock calibration. We simulated historical demographies under a Pleistocene climate model using observed genetic parameters. BSPs for these sequences showed rapid population growth after the Last Glacial Maximum (LGM) 18-20 k years ago and a flat population history during previous climate fluctuations. Population declines during the LGM appear to have erased signals of previous population fluctuations.

EVOLUTION OF ATLANTIC AND PACIFIC COD: LOSS OF GENETIC VARIATION AND GENE EXPRESSION IN PACIFIC COD

An allozyme investigation of 41 protein‐coding loci in two morphologically similar fishes, Atlantic and Pacific cod, indicates that Pacific cod experienced a severe population bottleneck that led to the loss of gene diversity and gene expression. Pacific cod possesses a significantly lesser amount of gene diversity (H = 0.032) than Atlantic cod (H = 0.125) and lacks gene expression for Me‐3. Allele‐frequency distributions differ between species as predicted by neutral theory: Atlantic cod has a U‐shaped distribution, which is expected for populations in drift‐mutation equilibrium, whereas Pacific cod has a J‐shaped distribution with an excess of low‐frequency alleles. This excess may be explained by the appearance of new alleles through mutation which have not yet reached intermediate frequencies through drift. The population bottleneck in Pacific cod was most likely associated with founder populations that dispersed into the Pacific Ocean after the Bering Strait opened. Under the molecular‐clock hypothesis a Nei genetic distance of 0.415 (based on 41 loci) suggests that Pacific cod dispersed into the Pacific Ocean soon after the Bering Strait opened in the mid‐Pliocene, 3.0 to 3.5 million years ago.

Comparative phylogeography of the ocean planet.

Understanding how geography, oceanography, and climate have ultimately shaped marine biodiversity requires aligning the distributions of genetic diversity across multiple taxa. Here, we examine phylogeographic partitions in the sea against a backdrop of biogeographic provinces defined by taxonomy, endemism, and species composition. The taxonomic identities used to define biogeographic provinces are routinely accompanied by diagnostic genetic differences between sister species, indicating interspecific concordance between biogeography and phylogeography. In cases where individual species are distributed across two or more biogeographic provinces, shifts in genotype frequencies often align with biogeographic boundaries, providing intraspecific concordance between biogeography and phylogeography. Here, we provide examples of comparative phylogeography from (i) tropical seas that host the highest marine biodiversity, (ii) temperate seas with high productivity but volatile coastlines, (iii) migratory marine fauna, and (iv) plankton that are the most abundant eukaryotes on earth. Tropical and temperate zones both show impacts of glacial cycles, the former primarily through changing sea levels, and the latter through coastal habitat disruption. The general concordance between biogeography and phylogeography indicates that the population-level genetic divergences observed between provinces are a starting point for macroevolutionary divergences between species. However, isolation between provinces does not account for all marine biodiversity; the remainder arises through alternative pathways, such as ecological speciation and parapatric (semiisolated) divergences within provinces and biodiversity hotspots.

Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.)

Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.

Genetic Population Structure and Origin of Life History Types in Chinook Salmon in British Columbia, Canada

Abstract We used protein electrophoresis to examine genetic population structure and origin of life history types of chinook salmon Oncorhynchus tshawytscha in British Columbia, Canada. Among 31 allozyme loci resolved in 91 samples from 63 populations of chinook salmon in rivers and hatcheries throughout British Columbia, population heterozygosities averaged 0.084 (range 0.048–0.108) and were typical of values for populations in other regions. A hierarchical gene diversity analysis indicated that 91.3% of the total allele-frequency diversity was attributable to within-population variability; the remaining 8.7% was attributable to geographic variability among populations, which was partitioned into among-river (3.3%), among-area (3.5%), and among-region (1.9%) components. Two major groups of populations appeared in the principal components analysis and in cluster analysis of genetic distances. A coastal group included populations in four subgroups: Central coast, Georgia Strait, lower Fraser River, and wes...

Changes in Size and Age of Chinook Salmon Oncorhynchus tshawytscha Returning to Alaska

The average sizes of Pacific salmon have declined in some areas in the Northeast Pacific over the past few decades, but the extent and geographic distribution of these declines in Alaska is uncertain. Here, we used regression analyses to quantify decadal trends in length and age at maturity in ten datasets from commercial harvests, weirs, and spawner abundance surveys of Chinook salmon Oncorhynchus tshawytscha throughout Alaska. We found that on average these fish have become smaller over the past 30 years (~6 generations), because of a decline in the predominant age at maturity and because of a decrease in age-specific length. The proportion of older and larger 4-ocean age fish in the population declined significantly (P < 0.05) in all stocks examined by return year or brood year. Our analyses also indicated that the age-specific lengths of 4-ocean fish (9 of 10 stocks) and of 3-ocean fish (5 of 10 stocks) have declined significantly (P < 0.05). Size-selective harvest may be driving earlier maturation and declines in size, but the evidence is not conclusive, and additional factors, such as ocean conditions or competitive interactions with other species of salmon, may also be responsible. Regardless of the cause, these wide-spread phenotypic shifts influence fecundity and population abundance, and ultimately may put populations and associated fisheries at risk of decline.

What maintains the central North Pacific genetic discontinuity in Pacific herring

Pacific herring show an abrupt genetic discontinuity in the central North Pacific that represents secondary contact between refuge populations previously isolated during Pleistocene glaciations. Paradoxically, high levels of gene flow produce genetic homogeneity among ocean-type populations within each group. Here, we surveyed variability in mtDNA control-region sequences (463 bp) and nine microsatellite loci in Pacific herring from sites across the North Pacific to further explore the nature of the genetic discontinuity around the Alaska Peninsula. Consistent with previous studies, little divergence (ΦST  = 0.011) was detected between ocean-type populations of Pacific herring in the North West Pacific, except for a population in the Yellow Sea (ΦST  = 0.065). A moderate reduction in genetic diversity for both mtDNA and microsatellites in the Yellow Sea likely reflects founder effects during the last colonization of this sea. Reciprocal monophyly between divergent mtDNA lineages (ΦST  = 0.391) across the Alaska Peninsula defines the discontinuity across the North Pacific. However, microsatellites did not show a strong break, as eastern Bering Sea (EBS) herring were more closely related to NE Pacific than to NW Pacific herring. This discordance between mtDNA and microsatellites may be due to microsatellite allelic convergence or to sex-biased dispersal across the secondary contact zone. The sharp discontinuity between Pacific herring populations may be maintained by high-density blocking, competitive exclusion or hybrid inferiority.

Understanding the adaptive consequences of hatchery-wild interactions in Alaska salmon

About 31% of salmon harvested in Alaska comes from the hatchery production of hundreds of millions of pink and chum salmon and smaller numbers of sockeye, Chinook, and coho salmon. The numbers of hatchery-reared juveniles released in some areas are greater than the numbers of juveniles from wild populations. However, virtually nothing is known about the effects of hatchery fish on wild populations in Alaska. Possible effects of these interactions can be inferred from studies of salmonids in other areas, from studies of other animals, and from theory. Numerous studies show a complex relationship between the genetic architecture of a population and its environment. Adaptive responses to nature and anthropogenic selection can be influenced by variation at a single gene, or more often, by the additive effects of several genes. Studies of salmonids in other areas show that hatchery practices can lead to the loss of genetic diversity, to shifts in adult run timing and earlier maturity, to increases in parasite load, to increases in straying, to altered levels of boldness and dominance, to shifts in juvenile out-migration timing, and to changes in growth. Controlled experiments across generations show, and theory predicts, that the loss of adaptive fitness in hatchery salmon, relative to fitness in wild salmon, can occur on a remarkably short time scale. All of these changes can influence survival and impose selective regimes that influence genetically based adaptive traits. The preservation of adaptive potential in wild populations is an important buffer against diseases and climate variability and, hence, should be considered in planning hatchery production levels and release locations. The protection of wild populations is the foundation for achieving sustained harvests of salmon in Alaska.

Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska

The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (Oncorhynchus keta) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.

How sedentary are greywing francolins (Francolinus africanus)

Phasianids are considered to be sedentary birds with limited dispersal so that populations may be expected to show genetic isolation by distance. To test this, we examined genetic variability in 618 greywing francolins (Francolinus africanus) at 24 localities over a 1,500 km2 area. We subdivided the samples to measure genetic population structure among localities separated by 6–60 km, and among coveys separated by 0.1–6 km. Thirteen of 30 (43%) allozyme loci were polymorphic, and heterozygosity ranged from 5.3 to 8.5% over 24 localities and averaged 7.0%, a value much larger than that found for other phasianids. Significant allele‐frequency heterogeneity was detected among localities and among coveys at several localities for several loci. Mantels test, however, showed that there was no correlation between geographical distance and the allele‐frequency difference between localities for all but one allele. Although spatial autocorrelation was detected with Morans I and Gearys c for two alleles, the geographical patterns of I in correlograms of 18 independent alleles showed a “crazy‐quilt” pattern of allele‐frequency patches. This shows that the isolation‐by‐distance model of subpopulation structure is inappropriate for these birds. Individuals, therefore, appear to disperse far beyond neighboring populations. “Private‐allele” and FST estimates of migration under the island model were 8–9 individuals between localities of each generation. Allele‐frequency heterogeneity, large amounts of gene flow, and the general lack of spatial autocorrelation imply that the small, socially‐structured populations of greywing are subject to high rates of turnover, founder effects, and random drift.