Nils Ryman

Genetic effects of harvest on wild animal populations

Human harvest of animals in the wild occurs in terrestrial and aquatic habitats throughout the world and is often intense. Harvest has the potential to cause three types of genetic change: alteration of population subdivision, loss of genetic variation, and selective genetic changes. To sustain the productivity of harvested populations, it is crucial to incorporate genetic considerations into management. Nevertheless, it is not necessary to disentangle genetic and environmental causes of phenotypic changes to develop management plans for individual species. We recommend recognizing that some genetic change due to harvest is inevitable. Management plans should be developed by applying basic genetic principles combined with molecular genetic monitoring to minimize harmful genetic change.

Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches

Population census size (NC) and effective population sizes (Ne) are two crucial parameters that influence population viability, wildlife management decisions, and conservation planning. Genetic estimators of both NC and Ne are increasingly widely used because molecular markers are increasingly available, statistical methods are improving rapidly, and genetic estimators complement or improve upon traditional demographic estimators. We review the kinds and applications of estimators of both NC and Ne, and the often undervalued and misunderstood ratio of effective-to-census size (Ne/NC). We focus on recently improved and well evaluated methods that are most likely to facilitate conservation. Finally, we outline areas of future research to improve Ne and NC estimation in wild populations.

Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals

Large-scale exploitation of wild animals and plants through fishing, hunting and logging often depends on augmentation through releases of translocated or captively raised individuals. Such releases are performed worldwide in vast numbers. Augmentation can be demographically and economically beneficial but can also cause four types of adverse genetic change to wild populations: (1) loss of genetic variation, (2) loss of adaptations, (3) change of population composition, and (4) change of population structure. While adverse genetic impacts are recognized and documented in fisheries, little effort is devoted to actually monitoring them. In forestry and wildlife management, genetic risks associated with releases are largely neglected. We outline key features of programs to effectively monitor consequences of such releases on natural populations.

Protection of intraspecific biodiversity of exploited fishes

Introduction page 417 What is special about aquatic conservation? 418 Differences between aquatic and terrestrial environments relative to conservation National sovereignty Amount of biodiversity Environmental continuity Anthropomorphism Invisibility Harvest Phenotypic variability Hybridization Releases Captive breeding Aquatic conservation is relatively neglected Genetic considerations in aquatic conservation 425 Threats to intraspecific genetic diversity Extinction Hybridization Genetic losses within populations Priorities for conservation in marine, anadromous and freshwater species Are marine species subjected to genetic degradation? Loss of genetic diversity in crashed populations What actions are needed to protect aquatic biodiversity? 436 Summary 439 Acknowledgements 439 References 439

Power for detecting genetic divergence: differences between statistical methods and marker loci

Information on statistical power is critical when planning investigations and evaluating empirical data, but actual power estimates are rarely presented in population genetic studies. We used computer simulations to assess and evaluate power when testing for genetic differentiation at multiple loci through combining test statistics or P values obtained by four different statistical approaches, viz. Pearsons chi‐square, the log‐likelihood ratio G‐test, Fishers exact test, and an FST‐based permutation test. Factors considered in the comparisons include the number of samples, their size, and the number and type of genetic marker loci. It is shown that power for detecting divergence may be substantial for frequently used sample sizes and sets of markers, also at quite low levels of differentiation. The choice of statistical method may be critical, though. For multi‐allelic loci such as microsatellites, combining exact P values using Fishers method is robust and generally provides a high resolving power. In contrast, for few‐allele loci (e.g. allozymes and single nucleotide polymorphisms) and when making pairwise sample comparisons, this approach may yield a remarkably low power. In such situations chi‐square typically represents a better alternative. The G‐test without Williamss correction frequently tends to provide an unduly high proportion of false significances, and results from this test should be interpreted with great care. Our results are not confined to population genetic analyses but applicable to contingency testing in general.

Patterns of distribution of biochemical genetic variation in salmonids: differences between species.

Abstract Using data from various sources, the genetic variability patterns at electrophoretically detectable loci were compared for four salmonid species, viz., Atlantic salmon ( Salmo salar ), brown trout ( Salmo trutta ), rainbow trout ( Salmo gairdneri ), and sockeye salmon ( Oncorhynchus nerka ). The absolute and relative importance of various sources of variation contributing to the total gene diversity were estimated hierarchically (e.g., within populations, between populations within rivers, between rivers, etc.). There are significant differences between the variability patterns of different species. For instance, a considerably larger portion of the total gene diversity is found within populations in the Atlantic salmon and the rainbow trout as compared to the brown trout. The implications of these findings are discussed in relation to different strategies for identification and utilization of existing genetic resources in different species.

Biocomplexity in a highly migratory pelagic marine fish, Atlantic herring

The existence of biologically differentiated populations has been credited with a major role in conferring sustainability and in buffering overall productivity of anadromous fish population complexes where evidence for spatial structure is uncontroversial. Here, we describe evidence of correlated genetic and life history (spawning season linked to spawning location) differentiation in an abundant and highly migratory pelagic fish, Atlantic herring, Clupea harengus, in the North Sea (NS) and adjacent areas. The existence of genetically and phenotypically diverse stocks in this region despite intense seasonal mixing strongly implicates natal homing in this species. Based on information from genetic markers and otolith morphology, we estimate the proportional contribution by NS, Skagerrak (SKG) and Kattegat and western Baltic (WBS) fish to mixed aggregations targeted by the NS fishery. We use these estimates to identify spatial and temporal differences in life history (migratory behaviour) and habitat use among genetically differentiated migratory populations that mix seasonally. Our study suggests the existence of more complex patterns of intraspecific diversity than was previously recognized. Sustainability may be compromised if such complex patterns are reduced through generalized management (e.g. area closures) that overlooks population differences in spatial use throughout the life cycle.

Unbiased estimator for genetic drift and effective population size.

Amounts of genetic drift and the effective size of populations can be estimated from observed temporal shifts in sample allele frequencies. Bias in this so-called temporal method has been noted in cases of small sample sizes and when allele frequencies are highly skewed. We characterize bias in commonly applied estimators under different sampling plans and propose an alternative estimator for genetic drift and effective size that weights alleles differently. Numerical evaluations of exact probability distributions and computer simulations verify that this new estimator yields unbiased estimates also when based on a modest number of alleles and loci. At the cost of a larger standard deviation, it thus eliminates the bias associated with earlier estimators. The new estimator should be particularly useful for microsatellite loci and panels of SNPs, representing a large number of alleles, many of which will occur at low frequencies.

Genetic relationships among landlocked, resident, and anadromous Brown Trout, Salmo trutta L.

Coexisting freshwater resident and anadromous (sea-run migratory) Brown Trout, Salmo trutta L., were compared genetically with landlocked populations (i.e. living above impassable waterfalls) in the same drainage system in western Norway. No genetic differentiation was found between resident and anadromous life-history types using the same locality and time for spawning. In contrast, significant genetic differences were found between Brown Trout (irrespective of life-history type) spawning in geographically separate localities, and particularly large differences were found between landlocked Brown Trout and those from localities accessible from the sea. These results are consistent with other multiple-locus studies of salmonid fishes, showing larger genetic differentiation between localities than between coexisting life-history types that differ in morphology and ecology.

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled a muscle transcriptome and then aligned genomic reads to the transcripts, creating an “exome assembly,” capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index FST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.