Distance-based population classification software using mean-field annealing

We describe a distance-based clustering method using a proximity matrix of genetic distances to partition populations into genetically similar groupings. The optimization heuristic mean-field annealing (MFA) was used to find locally optimal solutions where exhaustive search was not possible. To illustrate this method, we analysed both simulated and real data sets. Simulated data indicated that MFA successfully differentiated population groups, even with small F(ST) values, as long as there was separation of within and between group distances. Reanalysis of microsatellite data from various human populations using mean-fields found similar ethnic groups corresponding to major geographic regions reported by Rosenberg et al. (2002) who used the model-based computer program Structure. However, with MFA, the Kalash population was found to group with other Central/South Asian populations instead of being the only member of its own genetic cluster. Europe/Middle East populations formed a separate group from Central/South Asian populations instead of being a single group in the Structure analysis. The MFA analysis determined the greatest genetic distances (largest mean intracluster distance) occurred in native American populations, identifying three groups instead of only one found with Structure. For conservation purposes, it is not only important to identify genetically similar groupings but also to determine the relative level of genetic differentiation captured within these groups. To illustrate this, we compare two separate MFA analyses of Chinook salmon (Oncorhynchus tshawytscha) populations from British Columbia, Canada. The software called PORGS-MFA used in this article can be downloaded from http://www.pac.dfo-mpo.gc.ca/science/facilities-installations/pbs-sbp/mgl-lgm/apps/porgs/index-eng.htm.     

Evidence of successful recruitment of non-native pink salmon Oncorhynchus gorbuscha in Iceland

In mid-May 2022, pink salmon Oncorhynchus gorbuscha smolts were caught in the rivers Botnsá, Grímsá, and Langá in Iceland. This observation provides the first evidence of successful spawning and the completion of the freshwater phase of the life cycle in Icelandic rivers. It is the most western record of O. gorbuscha smolts in Europe, further west than Russia, Norway, and the UK. Smolts originating from Iceland potentially support the recruitment of this species in the North Atlantic and may lead to the establishment of a self-sustaining population in Iceland.     

Burying beetle Nicrophorus investigator reproduction on Pacific salmon carcasses

Abstract.  1. In many undisturbed watersheds along the Pacific Rim, anadromous salmon ( Oncorhynchus spp.) provide a predictable source of carrion to the riparian zone, largely due to horizontal transfer of salmon carcasses by bears ( Ursus spp.) and other vertebrates.
2. Burying beetles are important members of the north-temperate carrion fauna, and may utilise salmon carcasses and remnants for breeding. In this study, isotopic and observational data are reported that demonstrate previously unrecognised Nicrophorus investigator (Zetterstedt) reproduction on large salmon carcasses from five watersheds in coastal British Columbia.
3. Stable isotope signatures (δ¹⁵N and δ¹³C) of adult beetles collected in autumn indicate a diet of salmon origin in all but one individual from all watersheds, suggesting that this beetle–salmon association is widespread. Comparison of autumn isotope signatures to individuals collected randomly in summer suggests that isotope signatures represent the larval carrion source from the previous autumn rather than immediate adult diet.
4. In a survey of N. investigator use of salmon carcasses from two watersheds, 35 broods were observed on chum and pink salmon carcasses, including 16 natural brood complexes containing over 100 larvae, and five ranging from 250 to 750 larvae.
5. Overall, north-coastal populations of N. investigator breed on the rich and reliable salmon resource and may exhibit a system of communal breeding on these carcasses. This is most relevant when the dramatic reduction in salmon spawning biomass over the last century is considered.     

Evidence of a novel reproductive tactic in female kokanee Oncorhynchus nerka

Body composition analysis confirmed that egg development and reproductive senescence were delayed in silver female kokanee Oncorhynchus nerka (a small proportion of female kokanee exhibit extreme prespawning waiting and are called 'silvers' because of their colouration) relative to that of red female kokanee (most female kokanee exhibit this 'normal' phenology and are called 'reds'). Silver females were also smaller and younger than red females. A simple life-history model with two size thresholds is proposed to account for the observed body size and age differences. Adoption of the silver tactic by small females is proposed as a means to minimize intrasexual competition.     

Development of a flatbed passive integrated transponder antenna grid for continuous monitoring of fishes in natural streams

This paper describes a flatbed antenna grid designed for continuous remote monitoring of fish tagged with 23 mm passive integrated transponder (PIT) tags in a natural stream with extensive spatial coverage. A range of applications of the system is presented.     

Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.)

The prediction that selection affects the genome in a locus-specific way also affecting flanking neutral variation, known as genetic hitchhiking, enables the use of polymorphic markers in noncoding regions to detect the footprints of selection. However, as the strength of the selective footprint on a locus depends on the distance from the selected site and will decay with time due to recombination, the utilization of polymorphic markers closely linked to coding regions of the genome should increase the probability of detecting the footprints of selection as more gene-containing regions are covered. The occurrence of highly polymorphic microsatellites in the untranslated regions of expressed sequence tags (ESTs) is a potentially useful source of gene-associated polymorphisms which has thus far not been utilized for genome screens in natural populations. In this study, we searched for the genetic signatures of divergent selection by screening 95 genomic and EST-derived mini- and microsatellites in eight natural Atlantic salmon, Salmo salar L., populations from different spatial scales inhabiting contrasting natural environments (salt-, brackish, and freshwater habitat). Altogether, we identified nine EST-associated microsatellites, which exhibited highly significant deviations from the neutral expectations using different statistical methods at various spatial scales and showed similar trends in separate population samples from different environments (salt-, brackish, and freshwater habitats) and sea areas (Barents vs. White Sea). We consider these ESTs as the best candidate loci affected by divergent selection, and hence, they serve as promising genes associated with adaptive divergence in Atlantic salmon. Our results demonstrate that EST-linked microsatellite genome scans provide an efficient strategy for discovering functional polymorphisms, especially in nonmodel organisms.     

Genetic estimates of contemporary effective population size: to what time periods do the estimates apply?

Although most genetic estimates of contemporary effective population size (Ne) are based on models that assume Ne is constant, in real populations Ne changes (often dramatically) over time, and estimates (Ne) will be influenced by Ne in specific generations. In such cases, it is important to properly match Ne to the appropriate time periods (for example, in computing Ne/N ratios). Here I consider this problem for semelparous species with two life histories (discrete generations and variable age at maturity--the 'salmon' model), for two different sampling plans, and for estimators based on single samples (linkage disequilibrium, heterozygote excess) and two samples (temporal method). Results include the following. Discrete generations: (i) Temporal samples from generations 0 and t estimate the harmonic mean Ne in generations 0 through t - 1 but do not provide information about Ne in generation t; (ii) Single samples provide an estimate of Ne in the parental generation, not the generation sampled; (iii) single-sample and temporal estimates never provide information about Ne in exactly the same generations; (iv) Recent bottlenecks can downwardly bias estimates based on linkage disequilibrium for several generations. Salmon model: (i) A pair of single-cohort (typically juvenile) samples from years 0 and t provide a temporal estimate of the harmonic mean of the effective numbers of breeders in the two parental years (N b(0) and N b(t)), but adult samples are more difficult to interpret because they are influenced by Nb in a number of previous years; (ii) For single-cohort samples, both one-sample and temporal methods provide estimates of Nb in the same years (contrast with results for discrete generation model); (iii) Residual linkage disequilibrium associated with past population size will not affect single-sample estimates of Nb as much as in the discrete generation model because the disequilibrium diffuses among different years of breeders. These results lead to some general conclusions about genetic estimates of Ne in iteroparous species with overlapping generations and identify areas in need of further research.     

Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon

Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing approximately 89 kb we observed a frequency of 4.30 x 10(-3) SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.