Seabird mPVA (meta-Population Viability Analysis) Model:
An online tool to project abundance and quasi-extinction risk for IUCN Threatened Seabirds
The Seabird mPVA compares projected abundance and quasi-extinction risk under current conditions (no intervention) and various conservation scenarios, including removal of invasive species from specified breeding islands, translocation or reintroduction of individuals to an island of specified location and size, and at-sea mortality amelioration via reduction in annual at-sea deaths.
99 IUCN RedList Threatened (Critically Endangered, Endangered, Vulnerable) island breeding seabird species are included in the model. The Seabird mPVA is demographically structured and spatially explicit, and thus requires data on both seabird population characteristics and breeding locations. We developed a threatened seabird database (UCSC, 2020) which includes extensive information on seabird population status, trends, life history traits and threats. Data for breeding locations, island-based characteristics, and the presence of invasive species were extracted from the Threatened Island Biodiversity Database (TIB Partners, 2018). Detailed demographic data needed to parametrize our model were not available for all threatened seabird species. To estimate the required parameters we compilied empirically measured demographic data for related species and used Bayesian methods to estimate parameters required for the mPVA, including fecundity, stage-specific survival, annual breeding probability, and dispersal at the species-wide or species-island level. We standardize quasi-extinction thresholds based on literature review, but note that guidelines for quasi-extinction thresholds are variable for seabirds. Therefore, we chose thresholds that are considered conservative for large and rare species. We set quasi-extinction thresholds as 50 adult females for species with an initial population above 200 pairs, and 10 adult females for species with an initial population ≤ 200 pairs.
A detailed description of the Seabird mPVA model structure and mechanics can be found in Tinker et al. 2022.
How to use the Seabird mPVA
The Seabird mPVA online tool can be found HERE - https://nhydra.shinyapps.io/mPVA1/
Step 1. Select Species
Select your species of interest from the drop-down menu to view baseline projections
This will bring up the Baseline PVA Plots for your selected species (in this case, Rapa Shearwater).
TOP: Projected Vulnerability over 100 years expressed as the Mean Expected Quasi-Extinction Risk. The shaded areas are the 95% confidence intervals around the mean.
MIDDLE: Projected Trend in Abundance over 100 years expressed as the Mean Expected Abundance. The shaded areas are the 95% confidence intervals around the mean.
BOTTOM: Sample Simulations of the Trend in Abundance over 100 years
To examine the Baseline Projection values, click "Table 1. Baseline population projection" at the top of the graphs.
N_final: Species Abundance in 100 years
N_CILO: Species Abundance at the low 95% confidence interval in 100 years
N_CIHI: Species Abundance at the high 95% confidence interval in 100 years
P_QE_fin: Percent Quasi-Extinction Risk in 100 years (0.71 = 71%)
P_QE_LO: Percent Quasi-Extinction Risk at the low 95% confidence interval in 100 years
P_QE_HI: Percent Quasi-Extinction Risk at the high 95% confidence interval in 100 years
To examine which mean values were used in the model click on "Baseline Parameters" to the right of "Species Selection".
This table shows the baseline vital rates (means), and the breeding islands with the number of invasive species and total number of birds on each island.
Step 2: Evaluate Scenarios
Click "Evaluate Scenarios" in the top blue bar. This brings up the main evaluation interface.
You can change the number of replications of simulations as well as the number of simulations per replication. We suggest modifying these values to either 50/50 or 100/100; however, keep in mind that the greater number of replications and simulations, the greater amount of time it takes to compute the results (especially if the species breeds on numerous islands).
You have 3 options to evaluate scenarios: Invasive Species Eradiation, Translocation/Reintroduction, and At-Sea Mortality/Vital Rates.
Invasive Species Eradication
On the "Invasives" tab, to simulate an invasive species eradication simple uncheck the blue box that corresponds with the invasive species eradication you would like to conduct. You can conduct more than one eradication per simulation, uncheck as many boxes as you would like.
Click on the "Distribution" tab to add birds to a new or previously inhabited island.
The birds you add to the island are assumed to be juveniles, with an equal sex ratio
On this tab you can also update the number of birds on each breeding island by clicking on the number in the Nbirds column in the Current Island Populations table (note that these numbers are modeled population numbers and include all life stages).
Click on the "Mortality" tab to add/subtract at-sea mortality and/or adjust baseline vital rates.
Increases or reductions in at-sea deaths are assumed to affect both sexes and all independent age classes in proportion to their abundance.
Baseline vital rates can be adjusted for each parameter by sliding the bar with your mouse.
You can adjust the following vital rates: mean age first reproduction, adult breeding probability, hatching success, fledging success, first-year survival, sub-adult survival, adult survival, and environmental stochasticity.
You can simultaneously conduct an eradication, translocation, and update vital rates by simply updating values on all three tabs. Unfortunately, at this time, only one translocation/re-introduction can be modeled at a time.
Step 3: Run Simulations
Click on the blue "Run Simulations Now" button after you have visited all three evaluation tabs.
NOTE: You must click on all three tabs (Invasives, Distribution, Mortality) prior to clicking on "Run Simulations Now"
A box will pop up in the lower right-hand corner to with a status bar for the simulation
When the simulations are complete, the results will be plotted in green (line with 95% CI) on the plot with the baseline projections for both Projected Vulnerability (Quasi-Extinction Risk) and Projected Trend (Abundance).
For this example, we removed all invasive species from all breeding islands. You can see that the Quasi-Extinction Risk in 100 years is now close to zero (top graph - green line) and that the population now slightly increases in 100 years (bottom graph - green line).
To view the numerical data for the graphs, click on "Table 2: Projected Abundance, alternative scenarios"
After Year (1-100), the first six columns are the alternative scenario, the second six columns are the baseline projections
MNtot: Mean Species Abundance
TotN_LO: Species Abundance at the low 95% confidence interval
TotN_HI: Species Abundance at the high 95% confidence interval
MnPext: Mean Percent Quasi-Extinction Risk (0.71 = 71%)
Pext_LO: Percent Quasi-Extinction Risk at the low 95% confidence interval
Pext_HI: Percent Quasi-Extinction Risk at the high 95% confidence interval
MNtot_B: Mean Species Abundance
TotN_B_LO: Species Abundance at the low 95% confidence interval
TotN_B_HI: Species Abundance at the high 95% confidence interval
MnPext_B: Mean Percent Quasi-Extinction Risk (0.71 = 71%)
Pext_B_LO: Percent Quasi-Extinction Risk at the low 95% confidence interval
Pext_B_HI: Percent Quasi-Extinction Risk at the high 95% confidence interval
You can scroll down to see the values for all 100 years
The table can be downloaded by clicking "Download Table 2" at the top of the table
To run another scenario, simply modify the values you would like in one of the three evaluation tabs (Invasives, Distribution, Mortality), click on each of the three tabs, and then click "Run Simulations Now".
If any data on breeding islands, invasive species, or vitals rates is incorrect or needs to be updated, or if you have any questions about the model, please contact Kelly Zilliacus at firstname.lastname@example.org