Electronic supplementary material Field estimates of calf

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Electronic supplementary material
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Field estimates of calf-cow ratios
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On Wyoming elk winter ranges (Clarks Fork, Cody, and Jackson herds), classification
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surveys were conducted over 1-2 days via helicopter and ground observation, during late January
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and February. One or more observers counted the number of calves (< 1 y), adult females (> 1
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y), yearling bulls (1-2 y, spike-antlered), and adult bulls (>2 y, branch-antlered). The ratio of
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calves per 100 adult females is used by agencies and in our work as an index of calf recruitment.
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Though some studies have questioned the value of age ratios, they are considered comparatively
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reliable in the open habitats characteristic of our study area (1); moreover, a recent modeling
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study based on the life history of an elk population of the Greater Yellowstone Ecosystem (GY)
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indicated that changes in elk calf survival explained 93% of the variation in calf-cow ratios (2).
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On the winter range of the northern Yellowstone herd, which spans the boundary of Yellowstone
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National Park (YNP) including areas in both Wyoming and Montana, surveys are typically
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conducted in mid-March across a subset of 68 units that are stratified among four elevation
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sectors (see [3] for detailed survey methods). Where possible (Clarks Fork, Cody, and Jackson
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herds), we used a subset of the survey data taken from winter range where GPS collar
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information indicated elk were largely or entirely migratory (e.g., 4).
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To assess the timing of calf losses, we assembled calf-cow ratios conducted while the
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migratory elk subpopulations surveyed during winter were located on their high-elevation
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summer ranges inside YNP. The Clarks Fork herd was sampled by helicopter between
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September 14-22, 2007-2010 (n = 250-835) (4). The Cody herd was sampled by helicopter on
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August 13-14, 2011 (n = 1,376). Elk from the Jackson herd that summer inside YNP were
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sampled in August 1991, 2001, 2005, and 2010 (n = 713-1,311). Elk in the Dome Mountain
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herd, which comprises a major portion of the northern Yellowstone herd, were sampled in July
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and August 2007-2008 (n = 1,060) (5). Calf-cow ratios are prone to observation error and can be
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influenced by mixing of subpopulations in partially-migratory GYE elk, thus we present these
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data primarily to illuminate general patterns rather than to explore fine-scale inter-annual or
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inter-population variation. We assume that when summer ratios are similar to winter ratios in a
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given population, the majority of annual mortalities (due to all causes) have already occurred.
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Could historical predation rates have been biased low?
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It is possible that historical studies of grizzly bear foraging ecology underestimated the
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rate of elk calf predation, which could lead us to overestimate the dietary shift. An earlier study
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that tracked grizzly bears using VHF collars (6) may have had a lower probability of detecting
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elk calf predation events. Other past studies involving visual observations of grizzly bear activity
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described bouts of calf predation by individual bears in some localized areas, suggesting that calf
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predation might be more common (e.g., 7). However, the VHF-based study (6) used more
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systematic sampling involving a larger sample size of marked individual bears, over a larger
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geographic area and a longer study period – and ultimately the author applied a correction factor
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based on the amount of time grizzly bears spent at carcasses of varying size. Moreover, the
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apparent increase in grizzly bear predation on elk calves spans a period of steadily declining elk
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numbers (8), suggesting increasing selection for elk calves by grizzly bears.
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Simulated elk population growth rates and calf-cow ratios
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We explored the potential influence of changes in grizzly bear diets and elk calf predation
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rates on elk calf recruitment and population growth by generating a series of stochastic age-
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structured female-only population projection matrices. We assumed elk had five age classes (9):
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calves (0-1 y), yearlings (1-2 y), prime age adults (3-9 y), post-prime age adults (9-15 y) and old
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age adults (15+ y). We used a post-breeding census model (10), where elk in the 15+ age class
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continued to survive and reproduce. Each age class had different mean pregnancy and survival
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rates, and associated process variances (9) (Table 1). We assumed vital rates were beta
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distributed and constrained between 0.0 and maximum values (9) (Table 1).
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Because of uncertainty in the size of the elk population exposed to grizzly bear predation
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and in their vital rates over time, our goal in this analysis was to illustrate the potential
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magnitude of the demographic impact of increased grizzly bear predation on elk, not to simulate
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the specific dynamics of the elk population nor to account for all sources of demographic
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variation. Thus, we assumed that the only difference in elk vital rates before and after the
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cutthroat trout decline involved lower elk calf survival due to grizzly bear mortality. We
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assumed that calf mortality was a product of non-grizzly-related mortality (M) and grizzly
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predation (Pbt) prior to cutthroat trout decline, so that calf survival equaled:
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𝐶
𝑆𝑏𝑡
= (1 − 𝑃𝑏𝑡 )(1 − 𝑀),
eq. S1
For each matrix, we calculated the non-grizzly mortality (M) by rearranging Equation S1,
𝑆𝐶
𝑏𝑡
𝑀 = 1 − 1−𝑃
,
𝑏𝑡
eq. S2
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𝐶
where 𝑆𝑏𝑡
was the total (randomly drawn) calf survival rate. We calculated Pbt (calf mortality
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due to grizzly bears before cutthroat trout decline, i.e., “before trout”) as the number of calves
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eaten by grizzly bears per year over the total number of calves born. The total number of calves
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born equaled the starting population of calves (male and female) under a stable age distribution
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from a matrix of mean vital rate values. Both P and M were constrained so that they were
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between 0.0 and 1.0. The total population size (reported in Figure 4) including bulls was
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calculated assuming a 50:50 sex ratio of calves and yearlings, and a bull:cow ratio of 0.25
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(equivalent to the approximate mean bull:cow ratio across Wyoming elk herds; Wyoming Game
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and Fish Department, unpublished data).
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The calculation of the non-grizzly-related mortality (M) component of calf survival
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allowed us to estimate calf survival rate after the cutthroat trout decline by substituting the “post
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decline” predation rate (Pat) back into Equation 1 and calculating a new calf survival rate. This
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approach assumes that non-grizzly bear-related calf mortality rates were the same before and
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after the cutthroat trout decline. In other words (as discussed in the main text), we assumed that
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grizzly bear-related mortality was additive, and that calf mortality from other factors (i.e., other
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predators, malnutrition, etc.) did not change before and after the cutthroat trout decline. Grizzly
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bear predation is one of the only mortality factors that has been inferred to be largely additive in
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our study area (11).
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We examined two combinations of “pre-decline” and “post-decline” grizzly predation
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rates. One combination used a 1:1 nutritional equivalency of the cutthroat trout biomass lost
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from the diet with the elk calf biomass inferred to have replaced it (12; see main text for details),
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with a pre-decline predation estimate of 245 elk calves and a post-decline predation estimate of
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542 calves. Additionally, we calculated an estimate based on studies of grizzly bear kill rates
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(see main text) of 245 calves pre-trout-decline and 476 calves post-trout-decline. We calculated
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population growth rates for each matrix (pre- and post-decline) by taking the asymptotic lambda
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value (eigenvalue). We found the change in lambda by subtracting the pre-decline lambda value
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from the post-decline lambda value.
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To calculate the changes in expected calf-cow ratios across population sizes, we
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projected the population (at stable age distribution) eight months into the future, so that calves
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were eight months old, reflecting the approximate date (February 15th) when winter calf-cow
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ratios are collected in the field. We assumed that calf survival to eight months was a product of
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bear-related mortality and half of the annual non-bear-related mortality. For each iteration, we
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calculated the change in calf-cow ratios between the before and after trout declines.
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For each population size, we iterated the above procedure 1,000 times, using a different
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random set of vital rates for each run and we report the mean and 95% confidence intervals for
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the change in population growth rates and change in calf-cow ratios (Figure 4). All simulations
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were generated in program R (13). Beta values and eignevalues were simulated using the
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“popbio” package (14).
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References
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1. Bonenfant C, Gaillard JM, Klein F, & Hamann JL (2005) Can we use the young: female ratio
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to infer ungulate population dynamics? An empirical test using red deer Cervus elaphus as a
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model. J Appl Ecol 42(2):361-370.
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2. Harris NC, Kauffman MJ, & Mills LS (2008) Inferences about ungulate population dynamics
derived from age ratios. J Wildlife Manage 72(5):1143-1151.
3. Coughenour MB & Singer FJ (1996) Elk population processes in Yellowstone National Park
under the policy of natural regulation. Ecol Appl 6(2):573-593.
4. Middleton AD, et al. (In press) Animal migration amid shifting patterns of phenology and
predation: lessons from a Yellowstone elk herd. Ecology.
5. Cunningham JA, Hamlin KL, & Lemke TO (2008) Northern Yellowstone elk (HD313)
annual report. (Montana Fish, Wildlife, and Parks, Bozeman, MT).
6. Mattson DJ (1997) Use of ungulates by Yellowstone grizzly bears (Ursus arctos). Biol
Conserv 81(1-2):161-177.
7. Gunther KA & Renkin RA (1990) Grizzly bear predation on elk calves and other fauna of
Yellowstone National Park. In Bears: their biology and management (pp. 329-334).
8. Eberhardt LL, White PJ, Garrott RA, & Houston DB (2007) A seventy-year history of trends
in Yellowstone's northern elk herd. J Wildlife Manage 71(2):594-602.
9. Raithel JD, Kauffman MJ, & Pletscher DH (2007) Impact of spatial and temporal variation in
calf survival on the growth of elk populations. J Wildlife Manage 71(3):795-803.
10. Caswell H (2001) In Matrix population models: construction, analysis, and interpretation
(Sunderland, MA, USA, Sinauer Associates.
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11. Griffin KA, et al. (2011) Neonatal mortality of elk driven by climate, predator phenology and
predator community composition. J Anim Ecol 80(6):1246-1257.
12. Fortin JK, et al. (2013) Dietary adaptability of grizzly bears and American black bears in
Yellowstone National Park. J Wildlife Manage 77(2):270-281.
13. R Development Core Team (2011) R: a language and environment for statistical computing.
(Vienna, Austria, R Foundation for Statistical Computing.
14.Stubben C & Milligan B (2007) Estimating and analyzing demographic models using the
popbio package in R. J Stat Softw 22(11), 1-23.
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R code
## Although this program has been used by the U.S. Geological Survey (USGS), no warranty, expressed or implied,
is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and
related program material nor shall the fact of distribution constitute any such warranty, and no
responsibility is assumed by the USGS in connection therewith.
##This code is same as lambda analysis, except the lambdas for pre- and post-decline are calculated as (Nt+1)/Nt,
## where Nt is a population in SAD and Nt+1 is a population following a stochastic draw of vital rates, for both preand post-decline populations.
## All A matrices are post-breeding pulse models
rm(list=ls(all=TRUE))
library(MASS)
library(VGAM)
library(shape)
library(popbio)
##Thomas A. Morrison, Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming
##02.08.2012
##This routine generates a set of random elk population projection matrices before and after a decline in calf
##survival.
setwd()
#set.seed(11982)
reps = 1000
#number of runs per population size
pop = c(1350,2000, 2650, 3300, 3950)#, 4600, 5250) #2400,3000,3600,4200,4800,5400,6000)
#1200,1800,2400,3600,4200,female population sizes
sexratio = 0.5
#proportion of calves that are female
BCratio = 0.25
#ratio of adult cows (2+ y) to adult bulls (2+ y)
maxage = 15
#max age of elk
pred.mort1 = c(245,245) #245 estimated number of calves killed by grizzlies pre-decline based on median kill rate
from Mattson (1997)
pred.mort2 = c(542, 542) #estimated number of calves killed by grizzlies post-decline based on kill rate from
Fortin et al. (2013)
pred.mort3 = c(476)
#estimated number of calves killed by grizzlies after based on trout:calf biomass
equivalency calculations.
comp1 = 0.0161
comp2 = 0.0161
sc = 0.354; sy = 0.875; spa = 0.886; soa = 0.856; ss = 0.717 #age-class survival rates
fc = 0; fy =0.198; fpa = 0.928; foa = 0.864; fs = 0.530
#age-class fecundity rates
vrhi = c(0.729, 0.999, 0.999, 0.999, 0.900, 0.01, 0.250, 0.494, 0.475, 0.346)
#Max values allowed when
other vital rates are at best
vit.rates = cbind(c(0.354, 0.883, 0.886, 0.868, 0.724),
c(sqrt(0.02001),sqrt(0.00420),sqrt(0.002),sqrt(0.002),sqrt(0.00588)),
#Raithel et al. (2007) survival
estimates
#c(sqrt(0.03854),sqrt(0.00420),sqrt(0.00336),sqrt(0.00336),sqrt(0.00588)), #variance survival
c(0,0.198/2,0.928/2,0.864/2, 0.530/2),
#Pregnancy rates
c(0,sqrt(0.01508),sqrt(0.00126),sqrt(0.00250),sqrt(0.00647)))
#variance pregnancy
A = APre = APost1 = APost2 = matrix(0,maxage,maxage)
ran.beta1 = ran.beta2 = matrix(0,length(vit.rates[,1]),2) #"calf","yrlg","PA","OA","senes")
dater1 = dater2 = dater3 = dater4 = M.temp = M1.temp = NULL
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# Age classes: 0-1, 1-2, 2-9, 10-14, 15+
# Post-birth pulse matrix model to establish number of calves born to calculate P ####
A[1,] =
c(0,vit.rates[2,3]*vit.rates[2,1],rep(vit.rates[3,3]*vit.rates[3,1],8),rep(vit.rates[4,3]*vit.rates[4,1],4),vit.rates
[5,3]*vit.rates[5,1]) #preg * surv
A[2,1] = vit.rates[1,1] #calf
A[3,2] = vit.rates[2,1] #Yearlings
A[4,3] = vit.rates[3,1] #Prime-age adults
A[5,4] = vit.rates[3,1]
A[6,5] = vit.rates[3,1]
A[7,6] = vit.rates[3,1]
A[8,7] = vit.rates[3,1]
A[9,8] = vit.rates[3,1]
A[10,9] = vit.rates[3,1]
A[11,10] = vit.rates[3,1]
A[12,11] = vit.rates[4,1] #Old age adults
A[13,12] = vit.rates[4,1]
A[14,13] = vit.rates[4,1]
A[15,14] = vit.rates[4,1] #Senescent adults
A[15,15] = vit.rates[5,1]
p.stable = eigen.analysis(A, zero=TRUE)
for (k in 1:length(pop)) {
pop.N = p.stable$stable.stage*pop[k]
N.calves = p.stable$stable.stage[1]*pop[k]
Nt = sum(pop.N)+sum(pop.N[1:2])+(BCratio*sum(pop.N[3:maxage]))
##########
cc.temp = cc.diff = lam.diff1 = lam.diff2 = lam.diff3 = lam.diff4 = elast1 = elast2 = NULL
Pre1 = pred.mort1[1] / (N.calves/sexratio)
get female calf predation rate
if (Pre1 > 1) Pre1 = 1
Pre2 = pred.mort1[2] / (N.calves/sexratio)
if (Pre2 > 1) Pre2 = 1
Post1 = pred.mort2[2] / (N.calves/sexratio)
if (Post1 > 1) Post1 = .99
Post2 = pred.mort3[1] / (N.calves/sexratio)
if (Post2 > 1) Post2 = .99
#pre-decline low predation rate (least conservative) -- divide by 2 to
#pre-decline high predation rate (most conservative)
#post-decline low predation rate (least conservative)
#post-decline biomass intake (most conservative)
i=0
while (i<reps) {
for (j in (1:length(vit.rates[,1]))) {
repeat
{ ran.beta1[j,1] <- betaval(vit.rates[j,1],vit.rates[j,2])
if (ran.beta1[j,1] < vrhi[j]) break
}
}
for (j in (1:length(vit.rates[,1]))) {
repeat
{ ran.beta1[j,2] <- betaval(vit.rates[j,3],vit.rates[j,4])
if (ran.beta1[j,2] < vrhi[j+5]) break
}
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}
for (j in (1:length(vit.rates[,1]))) {
repeat
{ ran.beta2[j,1] <- betaval(vit.rates[j,1],vit.rates[j,2])
if (ran.beta2[j,1] < vrhi[j]) break
}
}
for (j in (1:length(vit.rates[,1]))) {
repeat
{ ran.beta2[j,2] <- betaval(vit.rates[j,3],vit.rates[j,4])
if (ran.beta2[j,2] < vrhi[j+5]) break
}
}
M = 1-(ran.beta1[1,1]/(1-Pre1)) #M isolates “natural” non-bear predation rate -- least conservative Npre grizzly =
95
M1 = 1-(ran.beta1[1,1]/(1-Pre2)) #M1 isolates “natural” non-bear predation rate -- most conservative Npre grizzly
= 304
if (M < 0 ) M = 0
if (M1 < 0 ) M1 = 0
M.temp = rbind(M.temp,M)
M1.temp = rbind(M1.temp,M1)
s.post1 = ran.beta1[1,1]
s.post2 = (1-M)*(1-Post1)
s.post3 = (1-M1)*(1-Post2)
S=c(s.post1,s.post2,s.post3)
#least conservative
#most conservative
#Post-birth pulse matrix model#
APre[1,] =
c(0,(ran.beta1[2,2]*ran.beta1[2,1]),rep(ran.beta1[3,2]*ran.beta1[3,1],8),rep(ran.beta1[4,2]*ran.beta1[4,1],4
),(ran.beta1[5,2]*ran.beta1[5,1])) #calf
APre[2,1] = S[1]
#calf S
APre[3,2] = ran.beta1[2,1] #yrling
APre[4,3] = ran.beta1[3,1] #PA
APre[5,4] = ran.beta1[3,1]
APre[6,5] = ran.beta1[3,1]
APre[7,6] = ran.beta1[3,1]
APre[8,7] = ran.beta1[3,1]
APre[9,8] = ran.beta1[3,1]
APre[10,9] = ran.beta1[3,1]
APre[11,10] = ran.beta1[3,1] #OA
APre[12,11] = ran.beta1[4,1]
APre[13,12] = ran.beta1[4,1]
APre[14,13] = ran.beta1[4,1]
APre[15,14] = ran.beta1[4,1]
APre[15,15] = ran.beta1[5,1] #senes
#Post-birth pulse matrix model pred rate -- least conservative#
APost1 <- APre
APost1[2,1] = S[2]
#APost1[1,] =
c(0,(ran.beta2[2,2]*ran.beta2[2,1]),rep(ran.beta2[3,2]*ran.beta2[3,1],8),rep(ran.beta2[4,2]*ran.beta2[4,1],4
),(ran.beta2[5,2]*ran.beta2[5,1])) #calf
#APost1[2,1] = S[2]
#calf S
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#APost1[3,2] = ran.beta2[2,1] #yrling
#APost1[4,3] = ran.beta2[3,1] #PA
#APost1[5,4] = ran.beta2[3,1]
#APost1[6,5] = ran.beta2[3,1]
#APost1[7,6] = ran.beta2[3,1]
#APost1[8,7] = ran.beta2[3,1]
#APost1[9,8] = ran.beta2[3,1]
#APost1[10,9] = ran.beta2[3,1]
#APost1[11,10] = ran.beta2[3,1] #OA
#APost1[12,11] = ran.beta2[4,1]
#APost1[13,12] = ran.beta2[4,1]
#APost1[14,13] = ran.beta2[4,1]
#APost1[15,14] = ran.beta2[4,1]
#APost1[15,15] = ran.beta2[5,1] #senes
ppost1 = eigen.analysis(APost1, zero=TRUE)
#calculates eignevalues and elasticities
Acomp1 = APost1[,]*(1+(comp1*(ppost1$elasticities[,]/max(ppost1$elasticities)))) #Increases the vital so that
lambda = 1.03
ppost1 = eigen.analysis(Acomp1, zero=TRUE)
#Post-birth pulse matrix model protein rate -- most conservative#
APost2 = APost1
APost2[2,1] = S[3]
#calf S
ppost2 = eigen.analysis(APost2, zero=TRUE)
#calculates eignevalues and elasticities
Acomp2 = APost2[,]*(1+(comp2*(ppost2$elasticities[,]/max(ppost2$elasticities)))) #Increases the vital so that
lambda = 1.03
ppost2 = eigen.analysis(Acomp2, zero=TRUE)
p.Pre = eigen.analysis(APre, zero=TRUE)
#calculates eignevalues and elasticities
p.Post1 = eigen.analysis(APost1, zero=TRUE) #calculates eignevalues and elasticities -- least conservative
p.Post2 = eigen.analysis(APost2, zero=TRUE) #calculates eignevalues and elasticities -- most conservative
APre.stable = eigen.analysis(APre, zero=TRUE)
NFpre = APre.stable$stable.stage*pop[k]
temp = 2*NFpre[1]*(1-Pre1)*((1-M)^(8/12))
NFpre = sqrt(APre)%*%NFpre
NFpre[1] = temp
ccpre = NFpre[1]/sum(NFpre[2:maxage])
APost1.stable = eigen.analysis(APost1, zero=TRUE) #least conservative
NFpost1 = APost1.stable$stable.stage*pop[k]
temp = 2*NFpost1[1]*(1-Post1)*((1-M)^(8/12))
NFpost1 = sqrt(APost1)%*%NFpost1
NFpost1[1] = temp
ccpost1 = NFpost1[1]/sum(NFpost1[2:maxage])
APost2.stable = eigen.analysis(APost2, zero=TRUE) #most conservative
NFpost2 = APost2.stable$stable.stage*pop[k]
temp = 2*NFpost2[1]*(1-Post2)*((1-M1)^(8/12))
NFpost2 = sqrt(APost2)%*%NFpost2
NFpost2[1] = temp
ccpost2 = NFpost2[1]/sum(NFpost2[2:maxage])
ccLeastCon = (ccpost1-ccpre)
ccMostCon = (ccpost2-ccpre)
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#Nt1.pre = sum(NFpre)+sum(NFpre[1:2])+(BCratio*sum(NFpre[3:maxage]))
#Nt1.post1 = sum(NFpost1)+sum(NFpost1[1:2])+(BCratio*sum(NFpost1[3:maxage]))
#Nt1.post2 = sum(NFpost2)+sum(NFpost2[1:2])+(BCratio*sum(NFpost2[3:maxage]))
lam.diff1 = rbind(lam.diff1, c(1,pop[k], p.Post1$lambda-p.Pre$lambda)) # #"low pred rate, least
conservative","Least",
lam.diff2 = rbind(lam.diff2, c(2,pop[k], p.Post2$lambda-p.Pre$lambda)) # #"biomass rate, most
conservative","Most",
cc.temp = rbind(cc.temp, c(ccpre,ccpost1,ccpost2))
cc.diff = rbind(cc.diff, c(ccMostCon,ccLeastCon))
i=i+1
}
temp1 = sort(lam.diff1[,3])
L95.d1 = temp1[reps*0.05]
U95.d1 = temp1[reps*0.95]
temp2 = sort(lam.diff2[,3])
L95.d2 = temp2[reps*0.05]
U95.d2 = temp2[reps*0.95]
temp3 = sort(cc.diff[,2])
L95.d3 = temp3[reps*0.05]
U95.d3 = temp3[reps*0.95]
temp4 = sort(cc.diff[,1])
L95.d4 = temp4[reps*0.05]
U95.d4 = temp4[reps*0.95]
dater1 = rbind(dater1,c(Nt,mean(lam.diff1[,3]),L95.d1,U95.d1))
dater2 = rbind(dater2,c(Nt,mean(lam.diff2[,3]),L95.d2,U95.d2))
dater3 = rbind(dater3,c(Nt,mean(cc.diff[,2]),L95.d3,U95.d3))
dater4 = rbind(dater4,c(Nt,mean(cc.diff[,1]),L95.d4,U95.d4))
}
Table legends
Table 1. Elk vital rate means and variances used in the elk population model.
Tables
Table 1
Age Class (years)
Survival
Variance
Max Survival
Pregnancy
Variance
Max Pregnancy
Calves (0-1)
0.354
0.02001
0.729
0.000
0.00000
0.000
Yearlings (1-2)
0.875
0.00420
0.999
0.198
0.01508
0.500
Prime age adults (2-9)
0.886
0.00200
0.999
0.928
0.00126
0.988
Post-prime adults (9-15)
0.856
0.00336
0.999
0.864
0.00250
0.950
Old adults (15+)
0.717
0.00588
0.900
0.530
0.00647
0.692
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