Beaufort trout MicroPlex: a high-throughput multiplex platform comprising 38 informative microsatellite loci for use in resident and anadromous (sea trout) brown trout Salmo trutta genetic studies.

A flexible panel consisting of 38 informative microsatellite markers for Salmo trutta is described. These markers were selected from a pool of over 150 candidate loci that can be readily amplified in four multiplex PCR groups but other permutations are also possible. The basic properties of each markers were assessed in six population samples from both the Burrishoole catchment, in the west of Ireland, and Lough Neagh, in Northern Ireland. A method to assess the relative utility of individual markers for the detection of population genetic structuring is also described. Given its flexibility, technical reliability and high degree of informativeness, the use of this panel of markers is advocated as a standard for S. trutta genetic studies.

Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua.

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

Balancing selection on MHC class I in wild brown trout Salmo trutta.

Evidence is reported for balancing selection acting on variation at major histocompatibility complex (MHC) in wild populations of brown trout Salmo trutta. First, variation at an MHC class I (satr-uba)-linked microsatellite locus (mhc1) is retained in small S. trutta populations isolated above waterfalls although variation is lost at neutral microsatellite markers. Second, populations across several catchments are less differentiated at mhc1 than at neutral markers, as predicted by theory. The population structure of these fish was also elucidated.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Pleistocene genetic legacy suggests incipient species of Sebastes mentella in the Irminger Sea.

To investigate a possible speciation event within the redfish (Sebastes mentella) complex in the Irminger Sea, we examined genetics, traditional morphology, geometric morphometrics and meristics of individuals sampled throughout the Sea. Tissue samples from 1901 fish were collected in 1995 and 1996 and from 1999 to 2002, and the fish were genotyped at nine microsatellite loci, two of which were developed for this study. Individual-based genetic analyses showed that two different gene pools exist in the Irminger Sea. Although these groups overlap extensively geographically, they segregate according to depth: those above and below 550 m. This signal of genotype distinction with depth was evident in both the earlier and later sampling. Historical imprints in the genetic data indicated that the redfish in the Irminger Sea are likely to represent a case of an incipient speciation event that began in allopatry during the Pleistocene glaciations followed by secondary contact. Although hybridization was observed between groups, an analysis of traditional and geometric morphometrics and of meristic variables suggested that restricted gene flow between the currently parapatric deep- and shallow-mesopelagic incipient species may be maintained by ecological isolation mechanisms.

Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland.

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.

The alpha-Gpdh polymorphism in the tick Ixodes ricinus: similar diurnal trends in genotypic composition in Irish and Swedish population samples.

Analysis of the alpha-Gpdh locus, coding for the enzyme alpha-glycerophosphate dehydrogenase (glycerol-3-phosphate dehydrogenase), was conducted using starch-gel electrophoresis on samples from one Irish and one Swedish population of the tick Ixodes ricinus. Morning ('AM') and late afternoon ('PM') samples of unfed adults were collected in each case. The results show a higher frequency of homozygotes in females in the AM than in the PM sub-samples in both populations. No such diurnal differentiation was found in the case of male ticks. The results are discussed in relation to previous studies on the polymorphism in Ireland and in the context of the known metabolic role of alpha-glycerophosphate dehydrogenase in insect muscle. The possible selective influence of climatological factors is considered.

A triose-phosphate isomerase polymorphism in the Atlantic salmon Salmo salar L.

Atlantic salmon, Salmo salar L., from four European locations show allelic variation at one of three triose-phosphate isomerase (TPI) loci (TPI-3*) when separated on horizontal starch gel electrophoresis, using either eye or liver extracts. Two common alleles (*100 and *103) and one rare allele (*97) segregate at TPI-3* with unambiguous typing being possible by observing the interlocus heterodimers. Family studies demonstrate that TPI-3* 100 and *103 are of autosomal location and are inherited in a Mendelian fashion. TPI-3* variation can also be typed in adipose fin tissue, allowing nondestructive tissue sampling. Three loci are also active in brown trout, Salmo trutta, with two individuals being homozygous for TPI-3*, as are a small number of S. salar from eastern Canada. The presence of this additional variable allozyme locus in S. salar is important, since genetic studies in that species have been limited by the low level of allozyme variability detectable.

The biochemical systematics of red and sika deer (genus Cervus) in Ireland.

Twenty enzyme loci were investigated using starch gel electrophoresis in managed populations of red deer (Cervus elaphus) and sika deer (C. nippon) from Ireland. The red deer, which originated from several European countries, were polymorphic (%P) at 25% of the loci examined and exhibited a mean heterozygosity (H) of 0.025. The sika, originally from Japan, were introduced to Ireland in very limited numbers. Here, %P was 5% and H was 0.006. Mean genetic distance (D) between these taxa was 0.160. Because Scottish red deer, the source of much of the Irish herd, had previously been investigated for 16 of the same enzyme loci, it was possible to merge the present data with results from that earlier study, which also included North American wapiti (C. elaphus canadensis). The resulting phenogram based on genetic distance demonstrates that sika are twice as distantly related to red deer and wapiti, than the latter are to each other and suggests that sika-like forms are ancestral. Also, the demonstration of absolute mobility differences in the products of two enzyme loci in red deer and sika has many practical applications.