William Stewart Grant

University of Alaska Fairbanks · College of Fisheries and Ocean Sciences

Amphiboreal taxa are often composed of vicariant phylogroups and species complexes whose divergence and phylogeographic affinities reflect a shared history of chronic isolation and episodic trans-Arctic dispersal. Ecological filters and shifting selective pressures may also promote selective sweeps, niche shifts and ecological speciation during col...

The genomic era continues to revolutionize our understanding about the evolution of biodiversity. In phycology, emphasis remains on assembling nuclear and organellar genomes, leaving the full potential of genomic datasets to answer long standing questions about the evolution of biodiversity largely unexplored. Here, we used Whole Genome Sequencing...

I had the privilege of being a part of fishery genetics from its start in the 1970s, when protein electrophoresis was first used to identify stocks of commercially important fishes and shellfishes. Research questions in fishery genetics have evolved tremendously over the past few decades, as new molecular techniques changed the nature of the questi...

Many Northeast (NE) Pacific fishes and invertebrates survived Pleistocene glaciations in northern refugia, but the extent that kelps survived in northern areas is uncertain. Here, we test the hypothesis that populations of sugar kelp (Saccharina latissima) persisted in the Gulf of Alaska during ice‐age maxima when the western margin of the Cordille...

The extent that Pleistocene climate variability promoted speciation has been much debated. Here, we surveyed genetic markers in winged kelp Alaria in the Gulf of Alaska, Northeast Pacific Ocean to understand how paleoclimates may have influenced diversity in this kelp. The study included wide geographic sampling over 2800 km and large sample sizes...

Pleistocene climate cycles greatly influenced the distributions of kelps in northern seas and gated trans-Arctic dispersals between the North (N) Pacific and N Atlantic oceans. Here, we used partial sequences of the mitochondrial DNA cytochrome oxidase I-5′ (COI) and plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit-3′ (rbcL) to...

Alaska has a diverse flora of seaweeds along its coast that can potentially support a substantial seaweed farming industry. Worldwide, seaweeds represent a more than $10 billion dollar industry that is expected to double by 2024. Kelps (brown seaweeds: Phaeophyta), in particular, are used in numerous products, ranging from food (including the foam...

We developed a hierarchical Bayesian model (HBM) to estimate missing counts of Chinook salmon (Oncorhynchus tshawytscha (Walbaum in Artedi, 1792)) at a weir on the Kogrukluk River, Alaska, between 1976 and 2015. The model assumed that fish passage during a breach of the weir was typical of passage during normal operations. Counts of fish passing th...

The origins of agriculture date to about 9000 years, but commercial culture and supplementation of marine populations reach back only a few centuries. Hence, wild populations still play a major role in seafood production. Closed culture, stock restorations, sea ranching and stock enhancements of marine fishes and invertebrates have been implemented...

Morphometry and otolith microchemistry point to the existence of two populations of the European anchovy (Engraulis encrasicolus) in the Bay of Biscay: one in open seawaters, and a yet unidentified population in coastal waters. To test this hypothesis, we assembled a large number of samples from the region, including 587 juveniles and spawning adul...

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 id...

The analyses of often large amounts of field and laboratory data depend on computer programs to generate descriptive statistics and to test hypotheses. The algorithms in these programs are often complex and can be understood only with advanced training in mathematics and programming, topics that are beyond the capabilities of most fisheries biologi...

The sustained exploitation of marine populations requires an understanding of a species' adaptive seascape so that populations can track environmental changes from short- and long-term climate cycles and from human development. The analysis of the distributions of genetic markers among populations, together with correlates of life-history and envir...

Graphical plot of fdist/Lositan [55, 56] simulation. Blue dots represent interpolation between mean values of FST and HE in each marker (microsatellite locus) analyzed. Blue dots falling within light grey area represent neutral markers whereas those within the yellow and the red areas represent outlier markers under balancing and directional select...

Summary of the microsatellite loci and primers for their PCR amplification used in the present study. (DOCX)

Pairwise comparisons of several differentiation genetics estimators. In S4A Table are showed values from G'ST and GST while in S4B Table the values from DEST. (DOCX)

In S5A Table are provided results from the assignment test for first generation migrants. The numbers within the table refer to the individuals that were allocated outside the sampling localities examined in this study (receiving sampling locations). The original sampling sites detected for each migrant are reported along the first row (native samp...

Pairwise estimates of LnRH values [60] for detecting loci under selection. Values in red are those exceeding the threshold of significance set at ±2.58. (DOCX)

Graphical plot of Hierarchical Island Model [59] simulations under the assumption of population structured in two (K = 2; S3A Fig) and three (K = 3; S3B Fig) clusters. Dots represent the interpolation between mean values of FST and HE in each marker (microsatellite locus) analyzed. Red, green and purple lines represent 1%, 5% and 95% percentiles of...

Contains information concerning the PCR multiplexing protocols, the genotyping procedures and the power analysis with different set of markers to detect genetic differentiation. (DOCX)

AMOVA on microsatellite DNA. Samples were divided into groups according to the bottom depth. (DOCX)

Values of the 13 environmental variables considered for each locality. (DOCX)

Summary of genetic variability observed at 14 microsatellite loci in the sampled locations. (DOCX)

The phylogeographic analysis of seaweeds faces numerous biological, methodological, and conceptual challenges. One challenge is to understand how life-history phases, mating systems, dispersal mechanisms, and physiological tolerances influence the distributions and persistence of local populations. A second challenge has been to develop genetic ass...

European anchovy (Engraulis encrasicolus, L) is a small teleost with major socio - economic importance that fuels research efforts . From a conservative perspective, the Bay of Biscay anchovy is especially relevant due to its recent stock collapse, whose biomass began to decline in 2002 and did not recover until 2010, after 5 years without fishing....

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red se...

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 spawn...

Sequence mismatch analysis (MMA) and Bayesian skyline plots (BSP) are commonly used to reconstruct historical demography. A survey of 173 research articles (2009-2014), which included estimates of historical population sizes from mtDNA or cpDNA, shows a widespread genetic signature of demographic or spatial population expansion in species of all ma...

Sequence mismatch analysis (MMA) and Bayesian skyline plots (BSP) are commonly used to reconstruct historical demography. A survey of 173 research articles (2009–2014), which included estimates of historical population sizes from mtDNA or cpDNA, shows a widespread genetic signature of demographic or spatial population expansion in species of all ma...

A major goal of phylogeographic analysis using molecular markers is to understand the ecological and historical variables that influence genetic diversity within a species. Here, we used sequences of the mitochondrial Cox1 gene and nuclear internal transcribed spacer to reconstruct its phylogeography and demographic history of the intertidal red se...

European anchovy is a small teleost with major socio-economic importance that fuels research efforts. The population genetic structure of this species has been much studied and previous studies, using molecular markers and otolith microstructure and chemistry, have suggested genetic heterogeneity for the Bay of Biscay anchovy; however, the extent o...

Apart from being commercially and socially significant, anchovies and sardines populations occupy crucial positions in the oceans’ ecosystems. Low in the food chain, clupeoids tend towards abundance, as if their purpose in life was to be eaten and fuel the upper levels of marine trophic chains. The present book covers a broad spectrum of topics on...

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 popul...

The State of Alaska established several salmon hatcheries in the 1970s with the intention of evening out natural population fluctuations. These hatcheries were later transferred to private-non-profit corporations, but under state production regulations. Permitted production levels have been expanded considerably in the last two decades, so that in...

The supplementation of natural populations of Pacific salmon Oncorhynchus spp. with hatchery fish poses unique management challenges. Two such challenges addressed in this study are limiting the number of hatchery fish spawning with natural-origin fish and maximizing the number of natural-origin fish in the supplementation broodstock. In this study...

The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, the...

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...

Observed patterns of genetic variability among marine populations are shaped not only by contemporary levels of gene flow, but also by divergences during historical isolations. We examined variability at 15 SNP loci and in mtDNA sequences (COI, 665 bp) in red king crab from 17 localities in the North Pacific. These markers define three geographical...

Observed patterns of genetic variability among marine populations are shaped not only by contemporary levels of gene flow, but also by divergences during historical isolations. We examined variability at 15 SNP loci and in mtDNA sequences (COI, 665 bp) in red king crab from 17 localities in the North Pacific. These markers define three geographical...

Hatcheries releasing chum salmon for ranching into Prince William Sound (PWS), Alaska, started in the 1970’s and increased dramatically in the late 1980’s. Currently, returning hatchery-produced chum salmon outnumber wild-produced fish by about 4 to 1 for a total return of 3.2 million hatchery-produced chum salmon. Some of these hatchery-originatin...

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 geog...

Summary of nuclear DNA SNP statistics in 626 samples of Engraulis encrasicolus by locus. Number of alleles or haplotypes for each locus (No alleles), Allelic Richness (A) for a minimum sample size of 15 individuals, mean heterozygosity (he) and FIS values with their Standard Error (SE). (DOCX)

The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconce...

The straying of hatchery salmon may harm wild salmon populations through a variety of eco-logical and genetic mechanisms. Surveys of pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon in wild salmon spawn-ing locations in Prince William Sound (PWS), Alaska since 1997 show a wide range of hatchery straying. The analysis of t...

The straying of hatchery salmon may harm wild salmon populations through a variety of ecological and genetic mechanisms. Surveys of pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon in wild salmon spawning locations in Prince William Sound (PWS), Alaska since 1997 show a wide range of hatchery straying. The analysis of the...

Nearest water distances (km) from sampled locations to pink and chum salmon hatcheries in PWS, Alaska. Districts names are 221 (Eastern), 222 (Northern) 225 (Eshamy), 226 (Southwestern) 227 (Montague,) 228 (Southeastern). Hatcheries are SGH (Solomon Gulch) CCH (Cannery Creek), WNH (Wally Noerenberg) and AFK (Armin F. Koernig) hatcheries.

Red king crab, a ‘deadliest catch’ species, supports the largest invertebrate harvest in Alaska. However, abundances of this crab have declined in several areas, leading to the closure of harvests in some areas, particularly in the Central Gulf of Alaska. Genetic information can support the management of red king crab by helping to define independe...

Patterns of population genetic differentiation can provide insights into both contemporary and historical gene flow, which may be useful for the management of exploited species.Isolation-by-distance (IBD) patterns may evolve relatively rapidly if dispersal is limited, while sharp breaks may reflect historical population isolation and secondary cont...

Climate change influences populations by reducing or extirpating local populations, by disrupting patterns of migration and by shifting geographical distributions. These events can affect genetic population structure in several ways. Molecular markers have been used in numerous population genetic and phylogeographical studies of marine species and...

Nucleotide sequence variation of mitochondrial DNA COI and nuclear rRNA gene regions was used to reconstruct phylogenetic relationships for the red-snow-crab species complex, including the red snow crab, Chionoecetes japonicus, its nominal subspecies, C. japonicus pacificus, and the triangle tanner crab, C. angulatus. The topologies of the Bayesian...

In the marine pelagic realm, the lack of prominent barriers to dispersal is thought to facilitate the connectivity of populations and prevent their genetic differentiation. Moreover, small pelagic fishes are generally characterized by large population sizes and consequently low levels of genetic drift. The “central-marginal” theory postulates that...

We assessed genetic differentiation among populations of weathervane scallop (Patinopecten caurinus) in the northeastern Pacific, extending over 2500km in the Gulf of Alaska and southeastern Bering Sea. Variability was surveyed at nuclear loci with allozyme, microsatellite, and single nucleotide polymorphism (SNP) methods, and at mitochondrial (mt)...

Grant, W. S., Spies, I., and Canino, M. F. 2010. Shifting-balance stock structure in North Pacific walleye pollock (Gadus chalcogrammus). – ICES Journal of Marine Science, 67: 1687–1696. High levels of gene flow are expected to produce genetic homogeneity among open-ocean populations of walleye pollock (Gadus chalcogrammus) because of few restricti...

Fifteen single-nucleotide-polymorphism (SNP) assays have been developed for red king crab (Paralithodes camtschaticus), a species which supports the ‘Deadliest Catch’ fishery in Alaska. Individual SNPs were discovered by 1) constructing a red king crab genomic DNA library, 2) sequencing a portion of 1339 random clones, 3) amplifying the homologous...

Understanding the spatial and temporal scales of connectivity between populations of marine organisms is important for defining units for management and conservation. Marine fishes and invertebrates generally differ from freshwater and anadromous species in having larger populations with greater potentials for gene flow. Nevertheless, shoreline top...

Abstract 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...

Aim Similar regimes of selection in different geographical settings can deterministically produce similar adaptive morphologies. We tested the hypothesis that the evolutionary trajectories of fish in upwelling zones can be altered by biogeographic contingencies in the biological and physical environment. Location Eastern Pacific and western Atlanti...

This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergi...

Grant, W. S., Merkouris, S. E., Kruse, G. H., and Seeb, L. W. 2011. Low allozyme heterozygosity in North Pacific and Bering Sea populations of red king crab (Paralithodes camtschaticus): adaptive specialization, population bottleneck, or metapopulation structure? – ICES Journal of Marine Science, 68: . Populations of red king crab in the North Paci...

Levels of neutral genetic diversity largely reflect effective population size (N(e)), which is influenced by physical and biological environmental variables. While large populations of marine fishes generally harbor higher diversities than freshwater species, historical demography or the effects of natural selection may significantly reduce N(e) an...