Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon.

The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region.

Erratum: Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA.

[This corrects the article DOI: 10.1093/ve/veaa054.].

Genomes reveal genetic diversity of Piscine orthoreovirus in farmed and free-ranging salmonids from Canada and USA.

Piscine orthoreovirus (PRV-1) is a segmented RNA virus, which is commonly found in salmonids in the Atlantic and Pacific Oceans. PRV-1 causes the heart and skeletal muscle inflammation disease in Atlantic salmon and is associated with several other disease conditions. Previous phylogenetic studies of genome segment 1 (S1) identified four main genogroups of PRV-1 (S1 genogroups I-IV).

Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies.

A novel application of genomewide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon () and then determined how two alternative management approaches for captive rearing affected variation at these loci.

A systematic surveillance programme for infectious salmon anaemia virus supports its absence in the Pacific Northwest of the United States.

In response to reported findings of infectious salmon anaemia virus (ISAV) in British Columbia (BC), Canada, in 2011, U.S. national, state and tribal fisheries managers and fish health specialists developed and implemented a collaborative ISAV surveillance plan for the Pacific Northwest region of the United States.

Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding.

Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations.

Parallel signatures of selection in temporally isolated lineages of pink salmon.

Studying the effect of similar environments on diverse genetic backgrounds has long been a goal of evolutionary biologists with studies typically relying on experimental approaches. Pink salmon, a highly abundant and widely ranging salmonid, provide a naturally occurring opportunity to study the effects of similar environments on divergent genetic backgrounds due to a strict two-year semelparous life history. The species is composed of two reproductively isolated lineages with overlapping ranges that share the same spawning and rearing environments in alternate years.

Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon.

Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometres, have become increasingly valuable in the presence of climate change, increasing hatchery production and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive data sets from spawning populations originating from across the species' range.

Inferring landscape effects on gene flow: a new model selection framework.

Populations in fragmented landscapes experience reduced gene flow, lose genetic diversity over time and ultimately face greater extinction risk. Improving connectivity in fragmented landscapes is now a major focus of conservation biology. Designing effective wildlife corridors for this purpose, however, requires an accurate understanding of how landscapes shape gene flow.

Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms.

Single nucleotide polymorphisms (SNPs) are appealing genetic markers due to several beneficial attributes, but uncertainty remains about how many of these bi-allelic markers are necessary to have sufficient power to differentiate populations, a task now generally accomplished with highly polymorphic microsatellite markers. In this study, we tested the utility of 37 SNPs and 13 microsatellites for differentiating 29 broadly distributed populations of Chinook salmon (n = 2783). Information content of all loci was determined by In and G'(ST), and the top 12 markers ranked by In were microsatellites, but the 6 highest, and 7 of the top 10 G'(ST) ranked markers, were SNPs.

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): natural replicate tests of post-Pleistocene evolution.

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere.

Recency, range expansion, and unsorted lineages: implications for interpreting neutral genetic variation in the sharp-tailed grouse (Tympanuchus phasianellus).

Both current and historical patterns of variation are relevant to understanding and managing ecological diversity. Recently derived species present a challenge to the reconstruction of historical patterns because neutral molecular data for these taxa are more likely to exhibit effects of recent and ongoing demographic processes. We studied geographical patterns of neutral molecular variation in a species thought to be of relatively recent origin, Tympanuchus phasianellus (sharp-tailed grouse), using mitochondrial control region sequences (CR-I), amplified fragment length polymorphisms (AFLP), and microsatellites.

Experimental studies of adaptive differentiation in Bahamian Anolis lizards.

Populations of the lizards Anolis carolinensis and A. sagrei were experimentally introduced onto small islands in the Bahamas. Less than 15 years after introduction, we investigated whether the populations had diverged and, if so, whether differentiation was related to island vegetational characteristics or propagule size.

MORPHOLOGICAL DIVERSIFICATION AND ADAPTIVE RADIATION: A COMPARISON OF TWO DIVERSE LIZARD CLADES.

We compared the morphological diversity (i.e., the amount of morphological space occupied) of two similar clades, the lizard genera Anolis and Sceloporus.