Population Level Variation of Atlantic Salmon in the Chalk Streams of Southern England and Neighbouring Regions

Abstract

In this thesis, population level variation is elucidated for Atlantic salmon living in the chalk streams of southern England – a unique and unusual habitat – as well as in immediately surrounding regions. Salmon in these chalk streams have yet to be robustly investigated, despite individual populations standing out from neighbouring populations in several previous studies. This thesis attempts to identify how different they are and the reasons for it. Then, this thesis also investigates the effect of this distinction on their internal population structure, as well as the current and future trajectory. A panel of microsatellite markers from the SALSEA-merge project were used to complete four studies of population structure in Atlantic salmon.

In the first study, which served primarily, as a training exercise, a multinational baseline was used to identify the origins of salmon recolonising the river Mersey in northwest England. Fish entering the Mersey originated from multiple sources, with the greatest proportion (45–60%) assigning to rivers in the geographical region just north of the Mersey, including Northwest England and the Solway Firth. The number of fish originating from proximal rivers to the west of the Mersey was lower than expected. The results suggested that the recolonisers were straying in accordance with the predominantly clockwise gyre present in the eastern Irish Sea.

In the second study, the relationship of salmon in the chalk streams of southern England to salmon outside this region was elucidated. Salmon from all five chalk streams in southern England with major salmon populations were found to all be genetically distinct from these neighbours and statistically less genetically diverse than salmon in southwest England and France. The reasons for this were relatively low immigration and a history of low effective population size.

In the third study, the extent of population structure of salmon between the chalk streams and within one chalk stream, the river Frome, was explored. The results suggested these salmon were divided into three groups, i.e. 1) the Frome & Piddle, 2) the Avon and 3) the Test & Itchen. A significant pattern of isolation by distance between salmon in these five rivers was also identified. Historic samples from the Avon were assigned to the contemporary three groups. Surprisingly, most of these fish assigned to the Frome and Piddle group. Within the river Frome, further sub-structure was identified over two separate years of sampling. Salmon from 2009 comprised three genetic groups, and salmon in 2011 comprised just two.

In the fourth study, historic scale samples were used to assess the current trajectory of genetic diversity and effective population size of salmon populations across Scotland, England, Wales and France. The majority of samples greater than 30 years old proved ineffective using the SALSEA panel. However, data was compiled from samples from eight rivers ranging from the Tweed in Scotland to the Scorff in France and from 1972 to 2012. Contrary to our hypothesis, most populations showed increases in allelic richness. Populations from one chalk stream show the steepest temporal decline in genetic diversity, which we speculate is partly due to the low immigration into the region. Effective population size proved difficult to determine using a number of methods and no robust pattern was identified.

Together these studies indicate that low immigration of salmon into the chalk streams appears to be key to their low genetic diversity and genetic distinction. Low immigration may also have enabled marked within-river population structure and the current negative trajectory of genetic diversity. The implications for general understanding of Atlantic salmon population structure across their range, and for the conservation of this species are discussed.