Pack: Relative importance of Chinook salmon abundance on resident Killer whale population viability pack

Created: 2014-08-29 11:04:10 Last updated: 2014-09-30 09:35:02

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Title: Relative importance of Chinook salmon abundance on resident Killer whale population viability pack

Description

The pack contains three workflows, 13 files and 2 documentations (tutorials to run the workflows).

Workflows:

1) Demography of the killer whales.

2) Resident killer whale-chinook salmon interactions.

3) Exploration of fishing scenarios.

These workflow uses input data of two different populations of Orcas in the northeastern Pacific Ocean of Canada and the U.S. But these workflows can also use input data from other populations of the Orcas in the world (see requirements for data entry in the documentation).

Two distinct populations of resident killer whales (Orcinus orca) in the northeastern Pacific Ocean have been identified in Canada and the U.S. as being of conservation concern. The Southern Resident Killer Whale (SRKW) population is currently listed as endangered under the U.S. Endangered Species Act on the grounds of its small population size and vulnerability to demographic stochasticity and catastrophic events such as oil spills (NMFS 2008). In Canada, under the Species At Risk Act (COSEWIC 2008), SRKW is listed as endangered due to its small and declining population size while the Northern Resident Killer Whale (NRKW) population is listed as threatened due to its small population size. The major threats identified for these two populations are nutritional stress associated with prey abundance levels and availability, particularly Chinook salmon (Oncorhynchus tshawytscha) (COSEWIC 2008, Ford et al. 2010a, 2010b), pollution and contaminants, and disturbances from vessels and sound (COSEWIC 2008, NMFS 2008). An important difference in the population-size trajectories of these two populations is that, in spite of their home range overlap and potential access to similar resources, SRKW has remained at a population size of less than 100 individuals for the last four decades with an average of 85 individuals in the last decade. NRKW population size has been generally increasing for the last four decades with 268 individuals at the end of 2011.

Vélez-Espino, L.A., John K.B. Ford, Eric Ward, Chuck K. Parken, Larrie LaVoy, Ken Balcomb, M. Bradley Hanson, Dawn. P. Noren, Graeme Ellis, Tom Cooney, and Rishi Sharma. 2013. Sensitivity of resident Killer Whale population dynamics to Chinook salmon abundance. Completion Report, Pacific Salmon Commission, Southern Boundary Restoration and Enhancement Fund, Vancouver BC. 191 p.

Vélez-Espino, L.A., Ford, J.K.B., Araujo, H.A., Ellis, G., Parken, C.K, & Balcomb, K. 2014. Comparative demography and viability of northeast Pacific resident killer whale populations at risk. Can. Tech. Rep. Fish. Aquat. Sci. 3084: vi + 56 p.

Vélez-Espino, L.A., John K.B. Ford, H. Andres Araujo, Graeme Ellis, Charles K. Parken and Rishi Sharma. 2014. Relative importance of Chinook salmon abundance on resident killer whale population growth and viability. Aquatic Conservation: Marine and Freshwater Ecosystems. Article first published online: 21 AUG 2014. DOI: 10.1002/aqc.2494.

The workflows can be run as well in: https://portal.biovel.eu/

Items (19)

File: ChinookAbundance_Data_R file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-08-29 12:04:57)

File: ChinookAbundance_FI_R file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-08-29 12:08:47)

File: Chinook_Ab_Definitions_R file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-08-29 11:54:07)

File: Chinook_Ab_Defs_FI_R file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-08-29 11:55:45)

File: Comparative Demography and Viability of Northeastern Pacific Resident Killer Whale Populations at Risk file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-11 09:03:39)

Description:

Comparative Demography and Viability of Northeastern Pacific Resident Killer Whale Populations at Risk.

L.A. Vélez-Espino, J.K.B. Ford, H.A. Araujo, G. Ellis, C.K. Parken, and K.C. Balcomb
Fisheries and Oceans Canada
Science Branch, Pacific Region
Pacific Biological Station
Nanaimo, BC
V9T 6N7
2014

Canadian Technical Report of
Fisheries and Aquatic Sciences 3084

Two distinct populations of resident killer whales (Orcinus orca) in the northeastern Pacific Ocean have been identified in Canada and the U.S. as being of conservation concern. In this paper we quantify the differences in demographic rates between southern residents (SRKW) and northern residents (NRKW) and merge perturbation and population viability analyses to study population responses to potential management actions targeting specific vital rates. The life cycles of these two populations were modeled as two-sex stage-structured models based on high-quality demographic data encompassing one killer whale generation (25 years; 1987-2011). Projection matrices were used to compute stochastic population growth and run stochastic simulations of extinction risk and recovery probabilities. Expected population growth rates are 0.91% annual decline (lambda = 0.9909; 95% CI: 0.9719-1.0081) for SRKW and 1.58% annual increase (lambda = 1.0158; 95% CI: 1.0027-1.0285) for NRKW. Conservatively, and under status-quo conditions, SRKW’s population size is expected to reach 75 individuals in a generation, with an extinction risk of 49% and an expected minimum abundance of 15 during a 100-year period, whereas NRKW’s population size could reach 400 individuals in a generation in the absence of density dependence, with an extinction risk of zero and an expected minimum abundance of 238 individuals during a 100-year period. SRKW’s lower realized and expected population growth as well as its lower viability relative to NRKW was mainly ascribed to SRKW’s lower production and survival of viable calves, lower proportion of juveniles transitioning into young reproductive females, and greater vital rate variances.

File: ER_Indicators file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-30 09:28:04)

Workflow: Exploration of fishing scenarios (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-26 11:25:42)

Description:

This workflow must run after the workflow: Resident killer whale-chinook salmon interactions. The interaction workflows generates a PostWorkspace file, this is a zip file and it is an R Workspace that transfers values from the Resident killer whale-chinook salmon interactions (main) workflow to the Exploration of fishing scenario (post-processing) workflow.

This workflow merges statistical inference derived from linkages between RKW vital rates (survival probability and fecundity rates) and chinook salmon abundance with demographic perturbation analysis and population viability analysis to address some of the pressing questions that have recently engaged the efforts of scientists and managers interested in: (1) the role of chinook salmon abundance in the population dynamics of RKW; and (2) how RKW population viability is expected to respond to changes in chinook mortality owing to harvest.

This workflow can be used to analyze interactions between chinook salmon abundance from specific stock aggregates and killer whale vital rates, the effect of these interactions on killer whale population growth, and the exploration of Chinook salmon fishing scenarios on killer whale population growth and short term projections of population size. See necessary input data.

To run this workflow in Taverna Workbench Biodiversity 2.5 requires an Rserve installation with the popbio, lattice, betareg, Formula and R.utils packages installed.

This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project and Fisheries and Oceans of Canada, BC, Canada. (http://www.pac.dfo-mpo.gc.ca/index-eng.html). BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.

References:

Workflow: Killer whale demography (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-24 13:48:03)

Description:

This workflow analyzes the demography and population growth of resident killer whale populations. Originally created for comparative studies of Northeastern Pacific populations at risk, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW), the workflow can be used for other killer whale populations or cetaceans counting with census data and life cycles that can be represented using the matrix models described in this document.

This workflow perform the following analyses:

• Vital rates estimation and probability distributions • Construction of Birth-flow Matrix Model • Eigen analysis • Elasticity analysis (deterministic and stochastic) • Damping time

To run this workflow in Taverna workbench, the users requires to have installed the Interaction Service plugin in Taverna. The workflow also requires an Rserve installation with the popbio, lattice, betareg, Formula and R.utils packages installed.

Related publications

Vélez-Espino, L.A., Ford, J.K.B., Araujo, H.A., Ellis, G., Parken, C.K, & Balcomb, K. Comparative demography and viability of northeast Pacific resident killer whale populations at risk. Can. Tech. Rep. Fish. Aquat. Sci. 3084: vi + 56 p.

File: Killer whale demography documentation (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-26 12:19:51)

Description:

This documentation contains the tutorial to run the Killer whale demography workflows.

This tutorial explains the type of input data needed to run the workflow. The corresponding analysis use data from two distinct O. orca populations in Canada, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW).

The Killer whale demography workflow performs the following analyses:

• Vital rates estimation and probability distributions

• Construction of Birth-flow Matrix Model

• Eigen analysis

• Elasticity analysis (deterministic and stochastic)

• Damping time

Two distinct populations of resident killer whales (Orcinus orca) in the north-eastern Pacific Ocean have been identified in Canada and the U.S. as being of conservation concern. The Southern Resident Killer Whale (SRKW) population is currently listed as endangered under the U.S. Endangered Species Act on the grounds of its small population size and vulnerability to demographic stochasticity and catastrophic events such as oil spills (NMFS 2008). In Canada, under the Species At Risk Act (COSEWIC 2008), SRKW is listed as endangered due to its small and declining population size while the Northern Resident Killer Whale (NRKW) population is listed as threatened due to its small population size. The major threats identified for these two populations are nutritional stress associated with prey abundance levels and availability, particularly Chinook salmon (Oncorhynchus tshawytscha) (COSEWIC 2008, Ford et al. 2010a, 2010b), pollution and contaminants, and disturbances from vessels and sound (COSEWIC 2008, NMFS 2008). An important difference in the population-size trajectories of these two populations is that, in spite of their home range overlap and potential access to similar resources, SRKW has remained at a population size of less than 100 individuals for the last four decades with an average of 85 individuals in the last decade. NRKW population size has been generally increasing for the last four decades with 268 individuals at the end of 2011.

File: Northern Resident Killer Whale (NRKW) demographic data (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-08-29 11:46:21)

File: Orcinus orca (Killer whale) demography and population viability analysis (PVA) documentation (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-08-29 12:21:47)

Description:

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.

The workflow only runs under Taverna workbench in Linux, coming soon will be available the version to run under Taverna workbench in Windows.

Therefore the documentation (tutorial to run the workflow) is only available for the Portal: https://portal.biovel.eu/

The Orcinus orca (Killer whale) demography and population viability analysis (PVA) workflow provides an environment to calculate a two-sex stage-structured matrix with no density dependence and to (i) quantify the differences in demographic rates between Orcinus orca population that explain population growth; (ii) to determine the relative influence vital rates on expected population growth; and, (iii) to generate projections of population size at various time horizons.

This workflow performs the following analyses:

• Vital rates estimation and probability distributions

• Construction of Birth-flow Matrix Model

• Eigen analysis

• Elasticity analysis (deterministic and stochastic)

• Damping time

• Stable stage distributions

• IID projection matrices representing discrete time periods

• Retrospective perturbation analysis

• Stochastic population growth from IID matrices and vital rate probability distributions

• Projections of population size.

Workflow: Resident killer whale-chinook salmon interactions (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-26 11:19:25)

Description:

The resident killer whale-chinook salmon interactions workflow provides an environment to calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates between killer whale (Orcinus orca) population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook (Oncorhynchus tshawytscha) abundance-vital rate interactions on expected population growth; (iii) to generate projections of population size at various time horizons.

This workflow perform the following analyses:

Vital rates estimation and probability distributions, Construction of Birth-flow Matrix Model, Eigen analysis, Elasticity analysis (deterministic and stochastic), Damping time• Stable stage distributions, IID projection matrices representing discrete time periods, Retrospective perturbation analysis, Stochastic population growth from IID matrices and vital rate probability distributions, Projections of population size, Regressions betwenn Killer WHale vital rates and stock-specific Chinook abundance, Elasticities of interactions between Killer Whale vital rates and stock-specific Chinook abundance.

This workflow comes in a package together with a tutorial, a second workflow and a group of inputs that belong two populations of killer whales. The inputs correspond to two distinct populations of resident killer whales (Orcinus orca) in the north-eastern Pacific Ocean. They have been listed in Canada and the U.S. as of conservation concern. The Southern Resident Killer Whale (SRKW) population is currently listed as endangered in both countries. The Northern Resident Killer Whale (NRKW) population has been listed as threatened in Canada.

To run this workflow in Taverna Workbench Biodiversity 2.5 requires an Rserve installation with the popbio, lattice, betareg, Formula and R.utils packages installed.

Related publications

File: Resident killer whale-chinook salmon interactions and Exploration of fishing scenarios documentation (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-26 12:09:48)

Description:

This documentation contains the tutorial to run two related workflows.

1. Resident killer whale-chinook salmon interactions workflow

The Resident killer whale-chinook salmon interactions workflow provides an environment to create calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates between Orcinus orca population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook abundance-vital rate interactions on expected population growth; (iii) to generate projections of population size at various time horizons.

http://www.myexperiment.org/workflows/4476.html

2. Exploration of fishing scenarios workflow

This workflow cannot be run without running first the Resident killer whale-chinook salmon interactions workflow. The Exploration of fishing scenarios workflow needs the PostWorkspace, a zip file generated by the first workflow. See details page 39, PostWorkspace (zip file).

This workflow merges statistical inference derived from linkages between resident killer whale (RKW) vital rates (survival probability and fecundity rates) and chinook salmon abundance with demographic perturbation analysis and population viability analysis to address some of the pressing questions that have recently engaged the efforts of scientists and managers interested in: (1) the role of chinook salmon abundance in the population dynamics of RKW; and (2) how RKW population viability is expected to respond to changes in chinook mortality owing to harvest.

This workflow can be used to analyse interactions between Chinook salmon abundance from specific stock aggregates and killer whale vital rates, the effect of these interactions on killer whale population growth, and the exploration of Chinook salmon fishing scenarios on killer whale population growth and short term projections of population size. See necessary input data.

http://www.myexperiment.org/workflows/4477.html

File: Sensitivity of resident killer whale population dynamics to Chinook salmon abundance file (Maria Paula Balcazar-Vargas)

Added by Maria Paula Balcazar-Vargas ... more than 1 year ago (2014-09-11 09:12:11)