Genetic stochasticity due to small population size contributes to population extinction, especially when population fragmentation disrupts gene flow. Estimates of effective population size (N e ) can therefore be informative about population persistence, but there is a need for an assessment of their consistency and informative relevance. Here we review the body of empirical estimates of N e for wild populations obtained with the temporal genetic method and published since Frankham's (1995) review. Theoretical considerations have identified important sources of bias for this analytical approach, and we use empirical data to investigate the extent of these biases. We find that particularly model selection and sampling require more attention in future studies.We report a median unbiased N e estimate of 260 (among 83 studies) and find that this median estimate tends to be smaller for populations of conservation concern, which may therefore be more sensitive to genetic stochasticity. Furthermore, we report a median N e /N ratio of 0.14, and find that this ratio may actually be higher for small populations, suggesting changes in biological interactions at low population abundances. We confirm the role of gene flow in countering genetic stochasticity by finding that N e correlates strongest with neutral genetic metrics when populations can be considered isolated. This underlines the importance of gene flow for the estimation of N e , and of population connectivity for conservation in general. Reductions in contemporary gene flow due to ongoing habitat fragmentation will likely increase the prevalence of genetic stochasticity, which should therefore remain a focal point in the conservation of biodiversity.

Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n ¼ 40) for which allele frequencies show parallel temperature-associated clines (p , 0.001, r 2 ¼ 0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted 'neutral' loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.

Effective population size (N e ) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of N e is crucial to management because it integrates genetic effectsPalabras Clave: deriva génica, metapoblación, método temporal, N e contempóranea, N e endogámica, N e varianza, proporción N e /N selección,suplementación basada en criaderos

The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy-Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model-based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high-saline North Sea and the low-saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.

Postglacial recolonisation patterns are well documented for the Northern Hemisphere biota, but comparable processes in the Southern Hemisphere have only recently been examined. In the largely terrestrial Northern Hemisphere, recession of ice after the Last Glacial Maximum (LGM) allowed various taxa, including slow-moving terrestrial species, to migrate poleward. By contrast, the Southern Hemisphere polar region is completely ringed by ocean, and recolonisation of Antarctica and the sub-Antarctic islands has thus presented considerable challenges. Although a few highly dispersive marine species have been able to recolonise postglacially, most surviving high-latitude taxa appear to have persisted throughout glacial maxima in local refugia. These contrasting patterns highlight the importance of habitat continuity in facilitating biological range shifts in response to climate change.

Numerically small but statistically significant genetic differentiation has been found in many marine fish species despite very large census population sizes and absence of obvious barriers to migrating individuals. Analyses of morphological traits have previously identified local spawning groups of herring (Clupea harengus L.) in the environmentally heterogeneous Baltic Sea, whereas allozyme markers have not revealed differentiation. We analysed variation at nine microsatellite loci in 24 samples of spring-spawning herring collected at 11 spawning locations throughout the Baltic Sea. Significant temporal differentiation was observed at two locations, which we ascribe to sympatrically spawning but genetically divergent 'spawning waves'. Significant differentiation was also present on a geographical scale, though pairwise F(ST) values were generally low, not exceeding 0.027. Partial Mantel tests showed no isolation by geographical distance, but significant associations were observed between genetic differentiation and environmental parameters (salinity and surface temperature) (0.001 < P < or = 0.099), though these outcomes were driven mainly by populations in the southwestern Baltic Sea, which also exhibits the steepest environmental gradients. Application of a novel method for detecting barriers to gene flow by combining geographical coordinates and genetic differentiation allowed us to identify two zones of lowered gene flow. These zones were concordant with the separation of the Baltic Sea into major basins, with environmental gradients and with differences in migration behaviour. We suggest that similar use of landscape genetics approaches may increase the understanding of the biological significance of genetic differentiation in other marine fishes.

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.

The spatial structuring of intraspecific genetic diversity is the result of random genetic drift, natural selection, migration, mutation, and their interaction with historical processes. The contribution of each has been typically difficult to estimate, but recent advances in statistical genetics have provided valuable new investigative tools to tackle such complexity. Using a combination of such methods, we examined the roles of environment (i.e., natural selection), random genetic processes (i.e., drift), and demography and life histories (e.g., feeding migrations) on population structure of a widely distributed and abundant marine pelagic fish of economic importance, Atlantic herring (Clupea harengus). Individuals were collected during peak spawning time from 19 spawning locations spanning the region from the western North Sea to the eastern Baltic Sea (N = 1859, eight microsatellite loci). We carried out separate analyses of neutral and selected genetic variation, which allowed us to establish that the two most important factors affecting population structure were selection due to salinity at spawning sites and feeding migrations. The genetic signal left by the demographic history of herring, on the other hand, seems to have been largely eroded, which is not surprising given the large reproductive potential and presumed enormous local effective population sizes of pelagic fish that constrain the effect of 4 Authors contributed equally.