Joseph L Thorley

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...

*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...

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...

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,...

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...

Invasive species are reducing global biodiversity. The Llgaay gwii sdiihlda—Restoring Balance project was initiated to halt and reverse biodiversity loss on six islands on Haida Gwaii, Canada through the eradication of invasive Sitka Black‐tailed deer ( Odocoileus hemionus sitkensis ). Invasive deer were killed using various hunting methods includi...

Kootenay Lake is a large, oligotrophic waterbody in southern British Columbia renowned for recreational fisheries for piscivorous rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus). Long-term datasets showed an increase in large-bodied (>2 kg) piscivore abundance followed by a collapse of the kokanee (Oncorhynchus nerka) pr...

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...

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,...

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...

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...

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...

Fig. S1. Bayesian estimates of the frequency of leks by count of male sage-grouse in a typical year with no oil and gas.

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.

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.

Fig. S3. Bayesian estimates (with 95% confidence intervals) of the carrying capacity in a typical year with no oil and gas by working group.

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.

Fig. S6. Bayesian estimates (with 95% credible intervals) of the effect of density on the density the subsequent year with no oil and gas.

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.

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.

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.

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.

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...

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...

Instructions on how to replicate the analyses

The spatial distribution of Bull Trout captures in the main lake by color-coded section Spatial information licensed under the Open Government License of British Columbia.

The spatial distribution of Rainbow Trout captures in the main lake by color-coded section Spatial information licensed under the Open Government License of British Columbia.

The spatial distribution of Rainbow Trout detections in the main lake by color-coded section Spatial information licensed under the Open Government License of British Columbia.

The spatial distribution of Bull Trout recaptures in the main lake by color-coded section Spatial information licensed under the Open Government License of British Columbia.

The spatial distribution of Bull Trout detections in the main lake by color-coded section Spatial information licensed under the Open Government License of British Columbia.

The spatial distribution of Rainbow Trout recaptures in the main lake by color-coded section Spatial information licensed under the Open Government License of British Columbia.

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,...

Instructions on how to replicate the analyses

Fish 21 on May 19th, 1998. Photograph by Alastair Thorne

Fish 21 on June 15th, 2002. Photograph by Alastair Thorne

Fish 21 on July 7th, 2006. Photograph by Alastair Thorne

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...

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...

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...

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...

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...