Joseph L Thorley

Joseph L Thorley
Poisson Consulting Ltd. · Research

PhD

About

110
Publications
14,579
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,351
Citations
Additional affiliations
January 2007 - September 2015
Poisson Consulting Ltd.
Position
  • Computational Biologist
January 2007 - September 2015
Poisson Consulting Ltd.
Position
  • Computational Biologist
May 2002 - September 2005
Scottish Government
Position
  • Stock Assessment Biologist
Education
September 1996 - September 2000
University of Bristol
Field of study
  • Theoretical Phylogenetics
September 1991 - June 1995
University of Oxford
Field of study
  • Biological Sciences

Publications

Publications (110)
Article
Stranding of fish due to flow reductions has been documented in the near shore of the Columbia and Kootenay Rivers, Canada, and can result in sub-lethal or lethal effects on fish. Ten years (1999–2009) of monitoring data have been collected at sites below two hydro-electric dams (Hugh-L-Keenleyside and Brilliant Dam) following flow reductions. A ge...
Article
Full-text available
*To whom correspondence should be addressed Summary: RadCon is a Macintosh® program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of tree...
Article
Spawning patterns in female brown trout Salmo trutta were examined by documenting the construction of nests in a small stream and later excavating them to recover progeny. The maternal provenance of nests was determined by genetic typing of embryos using microsatellite markers. Seventy-two nests, for which position and date of construction were kno...
Article
Full-text available
Using a simple example and simulations, we explore the impact of input tree shape upon a broad range of supertree methods. We find that input tree shape can affect how conflict is resolved by several supertree methods and that input tree shape effects may be substantial. Standard and irreversible matrix representation with parsimony (MRP), MinFlip,...
Article
The sand goby Pomatoschistus minutus is a major component of marine shelf and estuarine food webs and an important study organism in behavioural research. Yet, despite the sand goby's significance, its past and present patterns of migration and gene flow are poorly understood. Here we use the mtDNA control region and parts of the flanking tRNA gene...
Article
Full-text available
The species sensitivity distribution (SSD) is a statistical approach that is used to estimate either the concentration of a chemical that is hazardous to no more than x% of all species (the HCx) or the proportion of species potentially affected by a given concentration of a chemical. Despite a significant body of published research and critical rev...
Poster
Full-text available
Rainbow Trout are an important sport and food fish in the Columbia and Kootenay rivers, and their abundance is significantly influenced by hydroelectric activity in the region. Management of these salmonids in regulated rivers is facilitated by accurate estimates of egg deposition. Although spawner counts are conducted by observers on many systems,...
Article
Full-text available
Species sensitivity distributions (SSDs) are cumulative probability distributions that are used to estimate the percent of species that are affected by a given concentration of a chemical. The concentration that affects 5% of the species is referred to as the 5% Hazard Concentration (HC). Hazard concentrations are used for the derivation of environ...
Article
Full-text available
Understanding changes over historical timescales is essential to gauge conservation status of a species. Modern ecological data typically neglect past magnitudes of change, which fortunately can be evaluated by bridging disparate knowledge sources. We synthesized zooarchaeological, historical, traditional, and western science knowledge to document...
Article
Full-text available
Background: Spatial scale is important when studying ecological processes. The Greater sage-grouse (Centrocercus urophasianus) is a large sexually dimorphic tetraonid that is endemic to the sagebrush biome of western North America. The impacts of oil and gas (OAG) development at individual leks has been well documented. However, no previous studies...
Data
Fig. S1. Bayesian estimates of the frequency of leks by count of male sage-grouse in a typical year with no oil and gas.
Data
Table S2. The relative importance (wi) of the lag in areal disturbance due to well pads as a predictor of the count of males sage-grouse at individual leks. The relative importance is across all models with a lek distance of 0.8, 1.6, 3.2 and 6.4 km and the Pacific Decadal Oscillation index lagged one to four years.
Data
Table S3. The parameter estimates for the final lek count models with lower and upper 95% confidence/credible intervals. The estimates are for a lek distance of 3.2 km, areal disturbance due to well pads of one year and Pacific Decadal Oscillation index lag of two years. Model parameters are described in Table 1.
Data
Fig. S3. Bayesian estimates (with 95% confidence intervals) of the carrying capacity in a typical year with no oil and gas by working group.
Data
Fig. S4. Bayesian estimates (with 95% credible intervals) of the effect of the Pacific Decadal Oscillation index on the expected carrying capacity at a typical working group. The effect is the percent change in the expected carrying capacity relative to a Pacific Decadal Oscillation index value of 0.
Data
Fig. S6. Bayesian estimates (with 95% credible intervals) of the effect of density on the density the subsequent year with no oil and gas.
Data
Table S1. The relative importance (wi) of spatial scale as a predictor of the count of males sage-grouse at individual leks. The relative importance is across all models with the areal disturbance due to well pads and the Pacific Decadal Oscillation index both independently lagged one to four years.
Data
Fig. S2. Bayesian estimates (with 95% credible intervals) of the effect of year on the expected count of male sage-grouse at a typical lek after accounting for the Pacific Decadal Oscillation index and oil and gas.
Data
Fig. S5. Bayesian estimates (with 95% credible intervals) of the effect of year on the density the subsequent year after accounting for the Pacific Decadal Oscillation index and oil and gas.
Data
Table S4. The parameter estimates for the final population models with lower and upper 95% confidence/credible intervals. The estimates are for a lek distance of 3.2 km, areal disturbance due to well pads of one year and Pacific Decadal Oscillation index lag of two years. Model parameters are described in Table 1.
Article
Full-text available
Determining when fish spawn has major implications for effective fisheries management, particularly in dam-controlled rivers where reproductive potential may be affected by an altered hydrograph. Three methods for estimating spawn timing in riverine broadcast spawners were compared for their precision, effort and potential impact on a population of...
Article
Full-text available
Background Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports a...
Article
Full-text available
Background Ferox Trout are large, long-lived piscivorous Brown Trout ( Salmo trutta ). Due to their exceptionally large size, Ferox Trout are highly sought after by anglers while their life-history strategy, which includes delayed maturation, multiphasic growth and extended longevity, is of interest to ecological and evolutionary modelers. However,...
Technical Report
Full-text available
Each spring in the Lower Columbia River (LCR) below Hugh L. Keenleyside Dam (HLK) and in the Lower Kootenay River (LKR) below Brilliant Dam, thousands of Rainbow Trout (Oncorhynchus mykiss) spawn. Since 1992, BC Hydro has stabilized the spring discharge releases from HLK to protect Rainbow Trout redds from dewatering. Prior to the 1992 implementati...
Conference Paper
The construction and operation of Hugh L. Keenleyside Dam has changed the Columbia River ecosystem between the dam and the Canada-U.S. border. Between 2001 and 2013, Mountain Whitefish, Rainbow Trout, and Walleye were captured using boat electroshocking as part of an annual mark-recapture program designed to link changes in fish populations to inte...
Conference Paper
Full-text available
The Gerrard rainbow trout (Oncorhynchus mykiss) of Kootenay Lake are exceptionally large wild rainbow trout with trophy (>9 kg) individuals a relatively frequent occurrence during boom periods. However, to the consternation of anglers and guides, booms are punctuated by busts with a periodicity of approximately seven years. The current fishery regu...
Article
Full-text available
Biomass and production in the marine benthic community typically show rapid declines with bottom trawling. It has been postulated that such incidental reductions in prey abundance with trawling might negatively influence feeding success and hence the body condition of benthivorous fish. Length/weight and density by haul per year for six demersal fi...