Intraspecific genetic, morphological and life history structuring of brown trout (Salmo trutta) in a single complex catchment, the Foyle catchment

Rodger, Jessica Ruth (2017) Intraspecific genetic, morphological and life history structuring of brown trout (Salmo trutta) in a single complex catchment, the Foyle catchment. PhD thesis, University of Glasgow.

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Intraspecific genetic, morphological and life history structuring is evident in many taxa. Where such intraspecific structuring exists, study of the nature of the patterns displayed can reveal much about the evolutionary processes that operate during the early stages of divergence. Intraspecific structuring is particularly prevalent amongst fishes that occupy recently glaciated freshwater systems. One such species, the brown trout, Salmo trutta, was the subject of the work presented in this thesis.

Genetic and morphological intraspecific structuring of brown trout was examined across a single but large dendritic catchment, the River Foyle, Ireland. Structuring was examined at three spatial scales (large-scale, compared between major sub-catchments; medium-scale, compared between tributaries within sub-catchments; small-scale, compared between streams within tributaries). The two general aims of the study were to look for any structuring in either phenotype or genotype in brown trout across the catchment and, if this was found, to look for landscape or environmental gradients that might be driving such structuring.

Using a suite of 21 microsatellite markers that were chose for their ability to resolve population differences in this species elsewhere, this study identified clear and distinct genetic structuring. Brown trout collected from 28 sampling sites, resolved into 21 genetically distinct and discrete populations using a hierarchical approach implemented in STRUCTURE. The structuring was evidence across all three spatial scales. There was strong evidence of isolation by distance and isolation by environment playing a role in shaping the magnitude of the genetic differences between populations. Landscape variables which are shaped by anthropogenic impacts (urbanised area (measured as the number of houses in the catchment), proximity to farmland (measured as the distance to the nearest farm) and concentration of phosphorus in the water) showed the greatest effects in shaping the genetic population structuring (chapter 2).

In a parallel study, the morphological structuring of brown trout from across the Foyle catchment was investigated at three spatial scales. Morphology was measured as the shape of brown trout determined by Geometric Morphometric Analysis of fixed position landmarks identified on photographs of trout taken from 22 sampling sites across the catchment. Very clear, statistically significant differences in morphology (fish shape) were evident for all the 21 sampling sites (one sampling site was removed from the analysis due to small sample size) with Canonical Variate Analysis resolving 21 discrete phenotypic groups. Morphological structuring was evident across all spatial scales (large, medium and small). Analysis showed that genetic distance and geographic distance between morphological groups was significantly correlated with morphology of populations, with morphological groups that were most divergent from each other also being most genetically distinct and geographically more distant. The effect of landscape and environmental variables driving morphology of populations was tested. In-stream substrate composition, water pH, stream order, site elevation, river gradient and the number of houses per km2 (representative of urban area) were all found to have a significant effect on morphology of populations. However, once the effect on morphology on these environmental variables were accounted for the residual effect of genetic distance was not significant (chapter 3).

To attempt to discriminate between three alternative population genetic hypotheses for the origin of two alternative life history strategies in brown trout; freshwater residency and anadromy, the genetic structuring of brown trout was examined between life history strategy (anadromy or resident), between three sites and across two years (2013/2014) for brown trout collected from the Foyle catchment. There was no evidence of population structuring being attributed to life history strategy (that is no genetic differences between anadromous or resident trout). There was however strong and clear evidence of five genetic populations based on geographical site. Two sympatric populations were identified at each of two locations. However, both populations in each river were composed of both freshwater resident and anadromous brown trout, although the frequency of each life history strategy significantly differed between these rivers. The results of this study support the concept that partial migration in brown trout is most likely driven by a quantitative threshold trait, where the threshold trait value varies both between populations and between individuals within populations (chapter 4).

It is critical, for effective management of the relatively high economic value anadromous component of brown trout populations in a catchment, to be able to identify which tributaries are contributing most to their production. A Genetic Stock Identification (GSI) analytical framework was used to determine the tributary of origin for anadromous brown trout captured from a mixed stock within the River Faughan sub-catchment, River Foyle and to look for any evidence of straying. The results showed that three genetic populations from specific parts of the sub-catchment contributed disproportionately to the production of anadromous brown trout. There was also evidence of straying of anadromous trout, particularly to one tributary elsewhere in the catchment (chapter 5).

Taken together this body of work has demonstrated strong genetic and morphological structuring amongst brown trout in this large dendritic catchment. Genetic structuring seems to be at its most extreme when driven by factors which could be regarded as anthropogenic. This raises questions about human effects on the process of genetic divergence. Morphological structuring was, if anything even stronger than genetic structuring. Although there was evidence of genetic divergence between populations of differing morphologies, this neutral genetic differentiation was not a significant driver of morphological variation once landscape and environmental variables, such as substrate composition, driving morphological differences were taken into account. This suggests that the environmental drivers of structuring are greater in magnitude than neutral genetic divergence. Examining genetic structuring between two common morphologies of brown trout (anadromous and freshwater resident) in more detail, revealed no genetic differentiation between life history strategies but there was evidence of differences in frequency of life history between populations. Using the genetic structuring of brown trout as a genetic baseline it was possible to determine which tributaries within the River Faughan sub-catchment produce anadromous brown trout. If some discrete populations in a catchment are contributing disproportionately to the anadromous trout population (as they are in the Foyle) there is a strong risk of over exploitation and a need for enhanced attention in the nursery areas for those populations. These results have significant implications for the management of all trout in the Foyle catchment and elsewhere.

Item Type: Thesis (PhD)
Qualification Level: Doctoral
Keywords: Intraspecific, brown trout, genetic, population, morphology, life history, salmo trutta, structuring, genetic stock assignment.
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Colleges/Schools: College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
Funder's Name: European Commission (EC), Atlantic Salmon Trust (ATLSALTR)
Supervisor's Name: Adams, Professor Colin and Paulo, Professor Prodohl
Date of Award: 2017
Depositing User: Mrs Jessica Rodger
Unique ID: glathesis:2017-8522
Copyright: Copyright of this thesis is held by the author.
Date Deposited: 01 Nov 2017 10:12
Last Modified: 08 Nov 2017 08:48

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