StLircIi gel electrophoi-esis was used to study \-ariation at I I loci in mussels sampled mainly from British co'istal sites. Two types of mussel were identified, 2\f>sti"u ediilis, tlie common mussel rind its soutliern relatit e .\fvti/iir ga//n/~~,/,,or~iricin/i~. Se\ era1 partially dingnortic loci were used to miip tlie distrihtition of tlie t\vo forms. .\fvti/riJ ediilis \\as present ;it all sites sampled in Britain and Ireland hut \\as at low frequency in S\V England; .\I. ga//ul,ioi'incia/ir \vas detected in S\V England, tlie south and west of Ireland. Scotland and S E England. hut was absent from soutli \Vales. the Irish sea co;ists of tValt-s and Ireland. and SE England. Ap;irt fi-om tlie occurrence of . i f . gn//upinz,inrin/is in NE England. this distribution conforms bvith tlie results of studies using morphological characters and parallels the distrihution of many other soutlicrn species in Britain. At thc microgeographical l e d , .If. c d i i / i~ was foriitd to prcfrr more slieltered a n d rstiiarine conditions than :\I. ,~a//opmr,iiiria/i~. .Analysis rising the hest diagnostic loci sliowed that tiybridizati(in is occurring between .if, rdiilis and .\I. gn/lopiur~in~-ia/ir at all localities where the) occiir sympatrically hut that tlie extent of hybridization \aries considerahl) hetween localities. 'The distribution of localities ha\ ing Iiigli proportions of hybrid individuals is hest interpreted hy assuming that 11) hrids ha\ e higher fitness than parental tyries at these localities. :\ stlid! \v.is made o f \ ariation within and between those localities where only .\f. ~diilir indi\ idualsTvei-e ohser\.ed. Little significant geographic \.ariation in dlele frequency was detected, hut significcrnt deficits of 1ieteroz)gotes compared with H;irdy-lVeinberg expectations n e r e seen for most loci. .\n:ilysis suggests that the \Valilund effect is not involxd and that the most likely cause of tlie deficit is low frequencies (if niill 'illeles. In .\I. tdii/iJ no differences in phenotypic \.ariance in shell height and width v w e ohserved hetween samples of multiply lietcrozygoiis and multiply liomozygoiis individuals ;ind no qriietic differences were found bet\vern juveniles and adults. Overall little evidence was found t h a t Iialnncing selectinn is responsible for m'rintrn;ince of the polymoi-phisms studied in .if. edulir. 1 lie ~iatterii ofgcogr;ipliic \.ariation in gene frequencies in d i f v t i /~i s in the British Isles is discussed in relation to variation in tlie south and north of F.rirope and S o r t h . h e r i c a . It is concluded that steep clines in gene li-eqiiencies in .\I. idrrlis ohser\-ed h! otlier \viirkers in tlie Bnltir and in Long 1sl;ind Sound cannot tie .ittribiited to the presencr of .\I. gn//ol"ui,incin/i.

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This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.

BackgroundAnadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range.ResultsTo facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale.ConclusionsThis southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine en...