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Multi-season occupancy models identify biotic and
abiotic factors influencing a recovering Arctic
Peregrine Falcon Falco peregrinus tundrius population
JASON E. BRUGGEMAN,
1
* TED SWEM,
2
DAVID E. ANDERSEN,
3
PATRICIA L. KENNEDY
4
& DEBORA NIGRO
5
1
Minnesota Cooperative Fish and Wildlife Research Unit, Department of Fisheries, Wildlife and Conservation Biology,
University of Minnesota, St. Paul, MN 55108, USA
2
U.S. Fish and Wildlife Service, Fairbanks, AK 99701, USA
3
U.S. Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit, St. Paul, MN 55108, USA
4
Eastern Oregon Agriculture & Natural Resource Program, Department of Fisheries and Wildlife, Oregon State
University, Union, OR 97883, USA
5
Bureau of Land Management, Fairbanks, AK 99709, USA
Critical information for evaluating the effectiveness of management strategies for species
of concern include distinguishing seldom occupied (or low-quality) habitat from habitat
that is frequently occupied and thus contributes substantially to population trends. Using
multi-season models that account for imperfect detection and a long-term (1981–2002)
dataset on migratory Arctic Peregrine Falcons Falco peregrinus tundrius nesting along the
Colville River, Alaska, we quantified the effects of previous year’s productivity (i.e. site
quality), amount of prey habitat, topography, climate, competition and year on occupancy
dynamics across two spatial scales (nest-sites, cliffs) during recovery of the population. Ini-
tial occupancy probability was positively correlated with area of surrounding prey habitat
and height of nest-sites above the Colville River. Colonization probability was positively
correlated with nest height and negatively correlated with date of snowmelt. Local extinc-
tion probability was negatively correlated with productivity, area of prey habitat and nest
height. Colonization and local extinction probabilities were also positively and negatively
correlated, respectively, with year. Our results suggest that nest-sites (or cliffs) along the
Colville River do not need equal protection measures. Nest-sites and cliffs with historically
higher productivity were occupied most frequently and had lower probability of local
extinction. These sites were on cliffs high above the river drainage, surrounded by ade-
quate prey habitat and with southerly aspects associated with early snowmelt and warmer
microclimates in spring. Protecting these sites is likely to encourage continued occupancy
by Arctic Peregrine Falcons along the Colville River and other similar areas. Our findings
also illustrate the importance of evaluating fitness parameters along with climate and habi-
tat features when analysing occupancy dynamics, particularly with a long-term dataset
spanning a range of annual climate variation.
Keywords: Colville River Special Area, National Petroleum Reserve-Alaska, nest-site quality,
occupancy dynamics, population recovery, site colonization probability, site local extinction
probability.
Occupancy of habitats by animals is related to
resources such as food availability, shelter from
weather, protection from predators, availability of
mates and other factors that may affect the fitness
of individuals (MacKenzie et al. 2006, Mart
ınez
et al. 2006). Competition for these resources
affects wildlife distributions, with animals occupy-
ing higher-quality habitats initially, followed by
progressively lower-quality habitats (Fretwell &
*Corresponding author.
Email: brug0006@umn.edu
© 2015 British Ornithologists’Union
Ibis (2015), doi: 10.1111/ibi.12313
Lucas 1970, Petit & Petit 1996). Availability of
higher-quality habitats, in particular, affects sur-
vival and fecundity that, in turn, influences popu-
lation-level processes (Root 1998). Therefore,
understanding factors influencing occupancy of
these higher-quality habitats provides insights into
developing effective conservation and management
plans (Spencer et al. 2011).
Some of the greatest conservation successes of
the last century required an understanding of fac-
tors affecting occupancy and breeding success. For
example, population declines of raptors during the
1950s to 1970s owing to deleterious effects of
organochlorine pesticides, notably DDT, on repro-
ductive success resulted from a propagation of
effects from lower trophic levels (Ratcliffe 1970).
Understanding the effects of DDT, particularly on
birds, motivated management and conservation
efforts, including banning the use of DDT, pro-
tecting species and breeding habitats, reintroduc-
tion and translocation (Grier 1982, Rattner 2009).
Many raptor populations have recovered (e.g.
Sulawa et al. 2010) but some species remain
absent from their historical ranges or are in decline
(Kirk & Hyslop 1998), including the Northern
Harrier Circus cyaneus and California Condor
Gymnogyps californianus.
Peregrine Falcons Falco peregrinus were affected
by DDT through negative effects on reproductive
success, and breeding Peregrines were locally extir-
pated in many areas (Hickey 1969, Fyfe et al.
1976). Peregrine populations have since recovered
in many regions, augmented by a variety of efforts
beyond stopping use of DDT, including protection
under the U.S. Endangered Species Act (ESA),
captive rearing, fostering, use of hacking tech-
niques and reintroduction to eastern North Amer-
ica (Cade et al. 1988, 2003, but see Millsap et al.
1998). Peregrines require cliffs or tall structures
for nesting, and availability of suitable nest-sites is
a factor limiting breeding density and population
size (Newton 1988).
The Colville River and surrounding landscape
provides nesting habitat for a quarter of the Alas-
kan population of migratory Arctic Peregrine Fal-
cons Falco peregrinus tundrius, a subspecies that
breeds in Greenland, Arctic Canada and Alaska
north of the Brooks Range and on the Seward
Peninsula (White 1968, U.S. Department of the
Interior Bureau of Land Management 2008). Arc-
tic Peregrines were protected in 1970 under the
U.S. Endangered Species Conservation Act of
1969 and listed as endangered in 1973 under the
ESA (Swem 1994). In 1977, the Colville River
Special Area (CRSA) in the National Petroleum
Reserve-Alaska (NPR-A) was established to con-
serve Arctic Peregrine nesting and foraging habitat
while allowing activities such as oil and gas devel-
opment, recreation and research (U.S. Department
of the Interior Bureau of Land Management
2008). Sufficient recovery of Arctic Peregrines led
to their delisting in 1994 (Swem 1994); however,
protective regulations still exist under the CRSA
Management Plan to limit habitat loss and distur-
bance (U.S. Department of the Interior Bureau of
Land Management 2008). Measures also exist to
promote knowledge of Arctic Peregrine ecology,
including understanding which habitat features
influence occupancy of nest-sites (U.S. Depart-
ment of the Interior Bureau of Land Management
2008).
Our objective was to evaluate how intrinsic and
extrinsic factors influenced long-term trends in
Arctic Peregrine occupancy dynamics (MacKenzie
et al. 2003) in the CRSA to inform management
decisions and better understand Arctic Peregrine
ecology. We analysed nesting territory occupancy
dynamics using data from 22 years of Arctic Pere-
grine surveys along the Colville River initiated in
1981 when Arctic Peregrines were endangered and
continued through population recovery. We esti-
mated four parameters related to Arctic Peregrine
occupancy dynamics of both nest-sites and cliffs:
initial occupancy probability (k), colonization
probability (c), local extinction probability (x) and
detection probability (p; MacKenzie et al. 2003).
On the basis of previous research on Peregrines
(e.g. Grebence & White 1989, Olsen & Olsen
1989a,b, Ellis et al. 2004, Brambilla et al. 2006),
we made predictions to test relationships between
these parameters and biotic and abiotic covariates,
specifically climate, topography, previous year’s
productivity (as an index of site quality; hereafter
referred to as productivity), area of surrounding
prey habitat, competition and year (Table S1).
Our results provide information needed to assess
current protective regulations for Arctic Peregrines
in the CRSA (U.S. Department of the Interior
Bureau of Land Management 2008) and can be
used to improve management of Peregrine and
other raptor populations at northern latitudes.
They provide new information about factors
affecting nesting habits of Arctic Peregrines and
are applicable to other long-lived species with high
© 2015 British Ornithologists’Union
2J. E. Bruggeman et al.
site fidelity. Our study is also an example of the
analysis of an historical dataset using modern occu-
pancy methods that account for imperfect detec-
tion. Overall, we provide a quantitative
understanding of factors related to occupancy
dynamics of a recovering population and an
example for identifying frequently occupied, high-
quality habitats that will be the focus of conserva-
tion measures.
METHODS
Study area and data collection
Our study area consisted of the Colville River and
surrounding landscape in the CRSA, a 1-million-
hectare region located on Alaska’s North Slope
and within the NPR-A (Fig. 1). Oil and gas explo-
ration, recreation and research-related fieldwork
were the primary human activities in the CRSA
during our study, all of which were regulated to
limit impacts on Arctic Peregrines (U.S. Depart-
ment of the Interior Bureau of Land Management
2008). The CRSA contains numerous wetlands
with ground underlain by continuous permafrost.
Vegetation consists of tundra plant communities
except for the Colville River floodplain, where wil-
low Salix spp. and alder Alnus spp. communities
coincide with perennial herb pioneer communities
(Bliss & Cantlon 1957). The CRSA is character-
ized by short summers and long winters. Maxi-
mum average daily temperature during the nesting
period (May–August) ranged from 7.5 to 18.1 °C
(mean =11.9 °C0.52 se) from 1981 to 2002
at the Umiat National Oceanic and Atmospheric
Administration (NOAA) station (Fig. 1; 69°220N,
152°80W; National Oceanic and Atmospheric
Administration 2013) and Sagwon Natural
Resources Conservation Service (NRCS) SNOTEL
station (69°250N, 148°420W; Natural Resources
Conservation Service 2013). Minimum average
daily temperature during the same period ranged
from 2.4 to 4.9 °C (mean =0.29 °C0.38 se;
National Oceanic and Atmospheric Administration
2013, Natural Resources Conservation Service
2013). Duration of snow cover was 210–260 days
(mean =236 days 3 se; Hall et al. 2013,
National Oceanic and Atmospheric Administration
2013).
Arctic Peregrines are migratory and begin arriv-
ing at the CRSA in late April, nesting from May
to early August on cliffs, escarpments and bluffs
along the floodplain of the Colville River. Follow-
ing the fledging of young in August and Septem-
ber, Arctic Peregrines migrate to wintering areas
located from the southern USA south to Argentina
(Ambrose & Riddle 1988). We conducted surveys
for Arctic Peregrines by boat along the Colville
Figure 1. Study area in the Colville River Special Area (CRSA, grey shaded area), located on the North Slope of Alaska, USA, in
the National Petroleum Reserve-Alaska (inset). Annual surveys for nesting Arctic Peregrine Falcons were conducted along the Col-
ville River in the CRSA during 1981–2002. The location of the Umiat NOAA climate station is denoted. The Sagwon SNOTEL station
is located off the map to the east.
© 2015 British Ornithologists’Union
Arctic Peregrine Falcon occupancy dynamics 3
River in the CRSA from June to early August dur-
ing 1981–2002 and attempted to locate all Arctic
Peregrines breeding in the study area. We com-
pleted two surveys each year with the first occur-
ring during egg-laying and incubation in June, and
the second during the late July–early August nest-
ling period. Conducting two surveys annually
allowed us to account for nesting attempts that
failed and for birds becoming less detectable later
in the season. At each nest-site encountered, we
documented the presence of adults and estimated
the number of young in the nest (during survey
two), which we used as an index of productivity
(sensu Steenhof & Newton 2007). We mapped
each nest location onto a topographical map and
recorded the location with GPS when feasible.
We obtained GIS layers of elevation (U.S. Geo-
logical Survey 2011), land cover (Homer et al.
2004), surficial geology (Karlstrom 1964), aerial
imagery and streams in the CRSA. We used the
elevation layer to generate an aspect layer in ARC-
MAP 9.2. We used the land-cover layer to define
areas of open water, wetlands with woody vegeta-
tion and wetlands with emergent herbaceous vege-
tation, all of which serve as prey habitat in this
area (Ratcliffe 1993). Non-prey habitat land-cover
categories included areas dominated by sedges and
grasses, shrub/scrub, forest, barren/developed land
and ice/snow. Data on date of snowmelt were only
available for 1981–99 from the Umiat NOAA sta-
tion, so we obtained GIS snow-cover data for
2000–2002 from the MODIS/Terra snow cover 8-
day L3 global 500-m grid dataset (Hall et al.
2013). We gathered precipitation data for 1981–
2002 from the Umiat NOAA station (National
Oceanic and Atmospheric Administration 2013)
and Sagwon Natural Resources Conservation Ser-
vice SNOTEL station (Natural Resources Conser-
vation Service 2013).
Nest-site occupancy analysis
We used the multi-year dynamic occupancy model
of MacKenzie et al. (2003) to analyse trends in
individual nest-site occupancy. We defined y
ijt
as a
binary response variable denoting if we detected
Arctic Peregrines at nest-site iduring survey jof
year t.Wedefined nest-sites as any location where
we observed an Arctic Peregrine nest during any
year of our study. We defined parameters for the
probability nest-site ias: occupied in year 1 (w
i1
;
i.e. initial occupancy) and year t(w
it
); unoccupied
in year tand occupied in year t+1 (i.e. coloniza-
tion, c
it
); and occupied in year tand unoccupied
in year t+1 (i.e. local extinction, e
it
). We defined
p
ijt
as the probability that Arctic Peregrines were
detected at site iduring survey jof year t. After
estimating w
i1
, occupancy probability for other
years is w
t+1
=w
t
(1 e
t
)+(1 w
t
)c
t
(MacKenzie
et al. 2003).
We defined 12 covariates (Table 1) and used a
stepwise procedure (see Supporting Information for
further detail) to develop a candidate list of 24 mod-
els (e.g. Dugger et al. 2011). We centred and scaled
each covariate and used the Rpackage ‘unmarked’
(Fiske & Chandler 2011) in R2.15.2 (R Core Team
2012) to fit models to estimate covariate coefficients
for each parameter. We calculated an Akaike infor-
mation criterion (AIC) value for each model, and
ranked and selected the best-approximating models
using DAIC values (Burnham & Anderson 2002).
We calculated Akaike weights (w) for each model
to obtain a measure of model selection uncertainty
and model-averaged coefficients for covariates
included in models with DAIC <2 (Burnham &
Anderson 2002). We drew conclusions about
strength of evidence of relationships between
covariates and w
i1
,c
it
,e
it
and p
ijt
based on 95% con-
fidence intervals (CIs) of coefficients and the direc-
tion of relationships. We considered 95% CIs not
containing zero to indicate the strongest evidence of
relationships, 95% CIs that contained zero, but not
centred on zero, to indicate intermediate strength of
evidence, and 95% CIs centred on zero to indicate
little or no evidence of relationships (i.e. uninforma-
tive covariates; Arnold 2010).
Cliff occupancy analysis
We conducted a second occupancy analysis at a
larger spatial scale because Arctic Peregrines may
have used alternative nest-sites on the same cliff in
some years depending on the presence of other
Arctic Peregrines. As the breeding population of
Arctic Peregrines increased in the CRSA, spatial
patterns in nest-site occupancy changed (T. Swem
unpubl. data). During periods of lower Arctic
Peregrine abundance (i.e. early- and mid-1980s)
many cliffs along the entire river were unoccupied
and cliffs capable of supporting multiple pairs
were occupied by only one pair. Increasing popu-
lation size presumably led to competition for
nest-sites and use of multiple and alternative nest-
sites on cliffs. We divided nesting substrates (i.e.
© 2015 British Ornithologists’Union
4J. E. Bruggeman et al.
cliffs, escarpments, bluffs) along the Colville River
that had a history of at least one Arctic Peregrine
nest-site into 74 ‘cliff’segments using aerial ima-
gery and observations of topography during sur-
veys. Cliffs located upriver were discrete and
segment divisions were obvious (e.g. single cliff,
escarpment or bluff of limited extent). Cliffs
downriver were more extensive and we used the
presence of tributary drainages and streams as a
means of dividing cliffs and defining segments. We
defined a binary response variable, y
kjt
, denoting
whether Arctic Peregrines were detected at cliff k
during survey jof year t, and parameters for the
probability of initial cliff occupancy (w
k1
), occu-
pancy (w
kt
), colonization (c
kt
), local extinction
(e
kt
) and detection (p
kjt
; MacKenzie et al. 2003).
We defined 12 covariates (Table 1) and used a
stepwise procedure (see Supporting Information
for detail) to construct a candidate list of 48 mod-
els. We used the same methods as in the nest-site
occupancy analysis to fit models and rank and
select the best-approximating models.
Estimation of annual occupancy
probabilities
We used the best-supported models from the nest-
site and cliff analyses to calculate estimates of
annual occupancy probability (MacKenzie et al.
2003, Weir et al. 2009) for all nest-sites and cliffs
in the study area using package ‘unmarked’
(Fiske & Chandler 2011). We used non-parametric
Table 1. Definitions of covariates used in analyses examining factors related to nest-site and cliff occupancy dynamics of Arctic
Peregrine Falcons along the Colville River, Alaska, during 1981–2002. Listed are the scale(s) at which the covariates were evaluated;
subscripts for covariates are nest-site i, cliff kand year t.
Covariate Scale(s) Definition
height
i
Nest-site Height (m) of the nest-site above the Colville River
height
cliff,k
Cliff Average height (m) of nest-site(s) on cliff above the Colville River
meltdate
t
Nest-site; cliff Date of snowmelt in year t
aspect
i
Nest-site Categorical variable denoting the aspect of the nest-site (N, NE, NW, E, SE, S, SW, W)
aspect
cliff,k
Cliff Categorical variable denoting the average aspect of nest-site(s) on the cliff (N, NE, NW, E,
SE, S, SW, W)
peregrinedistance
it
Nest-site Distance (m) to nearest neighbouring occupied Arctic Peregrine nest in year t
precip
t1
Nest-site; Cliff Total accumulated precipitation (mm) from May to July in year t1
waterarea
i
Nest-site Total area (m
2
) of water and wetland prey habitat ≤3 km of nest-site. Bird and Aubry (1982)
and Enderson and Kirvin (1983) found >50% of Peregrine foraging flights were ≤3kmof
eyries
waterarea
cliff,k
Cliff Average total area (m
2
) of water and wetland habitat ≤3 km of cliff
productivity
i,t1
Nest-site Productivity (no. of young) of nest-site in year t1 as a measure of site quality
productivity
cliff,k,t1
Cliff Average productivity (no. of young) for nest-site(s) on the cliff in year t1
geology
k
Cliff Categorical variable denoting surficial geology type of cliff (Karlstrom 1964). Arctic Peregrines
used three types of surficial geology for nest-sites along the Colville River: (1) modern flood-
plain and associated low-terrace and alluvial fan deposits (Qfp); (2) coarse- and fine-grained
deposits associated with moderate to steep-sloped mountains and hills with bedrock
exposures largely restricted to upper slopes and crestlines (Qrb); and (3) dominantly
fine-grained
deposits associated with gently sloping hills with rare bedrock exposures (Qrc)
year Nest-site; Cliff Year tof the survey as a categorical value to assess whether differences existed in
colonization, local extinction and detection probabilities among years
yearlinear Nest-site; Cliff Year tof the survey as a numerical value to assess whether linear time trends existed in
colonization and local extinction probabilities as Arctic Peregrine population increased. Also
provides an index of time since DDT was banned
yearlog Nest-site; cliff Year tof the survey calculated as ln tto assess whether logarithmic time trends existed in
colonization and local extinction probabilities as Arctic Peregrine population increased. Also
provides an index of time since DDT was banned
yearthreshold Nest-site; cliff Year tof the survey calculated as t/(1 +t) to assess whether time trends existed as a
threshold function related to colonization and local extinction probabilities as Arctic Peregrine
population increased. Also provides an index of time since DDT was banned
survey
it
Nest-site Survey no. one or two of the nest-site during year t
survey
kt
Cliff Survey no. one or two of the cliff during year t
© 2015 British Ornithologists’Union
Arctic Peregrine Falcon occupancy dynamics 5
bootstrap techniques (Efron & Tibshirani 1993) to
calculate standard errors of annual occupancy esti-
mates by using the ‘nonparboot’function in pack-
age ‘unmarked’(Fiske & Chandler 2011) and 100
bootstrap samples for each year. Because we used
data from year t1 to parameterize models for
year t, we only estimated occupancy for 1982–
2002.
RESULTS
The total maximum number of adult Arctic Pere-
grines estimated during surveys increased during
our study, ranging from 27 birds in 1982 to 121
birds in 1998 (mean =83.5 6.2 se, n=22).
The number of nest-sites at which we detected
Arctic Peregrines ranged from 28 in 1981–83 to
69 in 2001 (mean =52 3.1 se, n=22, Fig. 2).
During 22 years of surveys we detected Arctic
Peregrines in 108 unique nest-site locations, 11
nest-sites were occupied only once in the
22 years and three nest-sites were occupied every
year.
The number of cliffs on which we detected
Arctic Peregrines ranged from 25 in 1981 to 52 in
2000 (mean =40 1.8 se, n=22, Fig. 2). Nine
cliffs were occupied only once during the 22-year
study, whereas 11 cliffs were occupied every year.
Across all years of surveys of 74 cliffs, the maxi-
mum number of nest-sites per cliff ranged from 1
to 5 (mean =1.5 0.11 se, n=1628), the mini-
mum number of adult Arctic Peregrines counted
per cliff ranged from 0 to 2 (mean =0.24 0.07
se, n=74) and the maximum number of adult
Arctic Peregrines counted per cliff ranged from 1
to 10 (mean =2.8 0.20 se, n=74). We provide
a summary of covariate values in Table S2.
Nest-site occupancy analysis
There were 14 best-approximating models with
DAIC <2; the model with the most support had
w=0.112 (Table S3). Initial occupancy was posi-
tively correlated with nest-site height and area of
surrounding prey habitat with intermediate sup-
port (Table 2). Colonization was positively and
strongly related to nest-site height (Fig. 3a), year
as a logarithmic function and year as a threshold
function (Table 2). Colonization was negatively
correlated with distance to the nearest neighbour-
ing Arctic Peregrine nest with intermediate sup-
port (Fig. 3b). Local extinction was negatively and
strongly related to area of surrounding prey habitat
(Fig. 3c), nest-site productivity in the previous
year (Fig. 3d), year as a logarithmic function and
year as a threshold function (Table 2). Detection
probability varied with year and was lower during
the second surveys within each year (survey
it
coef-
ficient estimate =0.571, 95% CI =0.821,
0.321; Fig. S1a). Annual occupancy probability
estimates for all 108 nest-sites in the study area
during 1982–2002 ranged from 0.264 in 1983 to
0.645 in 2001 (mean =0.504 0.028 se;
Fig. S2).
0
10
20
30
40
50
60
70
1980 1982 1984 1986 1988 1990 1992 1994 1996 1998 2000 2002
Number of occupied nest-sites or cliffs
Year
Nest-sites
Cliffs
Figure 2. Temporal trends in the number of occupied nest-sites and cliffs by nesting Arctic Peregrine Falcons enumerated during
surveys along the Colville River in the Colville River Special Area, Alaska, between 1981 and 2002.
© 2015 British Ornithologists’Union
6J. E. Bruggeman et al.
Cliff occupancy analysis
There were nine best-approximating models with
DAIC <2; the model with the most support had
w=0.078 (Table S4). Initial occupancy was posi-
tively and strongly correlated with average nest-site
height on the cliff and area of surrounding prey
habitat (Table 3, Fig. 4a,b). Colonization was posi-
tively and strongly associated with average nest-site
height (Fig. 4c), year as a logarithmic function and
year as a threshold function, and negatively and
strongly correlated with date of snowmelt (Fig. 4d)
and surficial geology type Qfp (Table 3). Coloniza-
tion was positively correlated with surficial geology
type Qrb with intermediate support. Local extinc-
tion was negatively and strongly correlated with
average nest-site height, area of surrounding prey
habitat, average nest-site productivity on the cliff
Table 2. Model-averaged covariate coefficient estimates (and 95% CI) from the best-approximating models (Table S3) from the anal-
ysis examining factors related to nest-site occupancy dynamics of Arctic Peregrine Falcons along the Colville River, Alaska, during
1981–2002. The response variable was y
ijt
, a binary variable denoting whether Arctic Peregrines were detected at nest-site iduring
survey jof year t. Covariates are defined in Table 1. Bold and italicized estimates indicate the covariate had strong and intermediate
support, respectively. n/a indicates the covariate was not included in the best-approximating models for that parameter.
Parameter
Covariate Initial occupancy probability Colonization probability Local extinction probability
height
i
0.805 (0.192, 1.80) 0.693 (0.310, 1.08) 0.057 (0.410, 0.296)
waterarea
i
0.701 (0.371, 1.77) 0.261 (0.168, 0.691) 0.524 (0.936, 0.112)
peregrinedistance
it
n/a 0.772 (1.60, 0.055) n/a
productivity
i,t1
n/a n/a 0.712 (1.02, 0.402)
precip
t
n/a n/a 0.209 (0.588, 0.170)
yearlog n/a 0.341 (0.133, 0.548) 0.387 (0.629, 0.146)
yearthreshold n/a 2.84 (1.16, 4.51) 2.52 (4.22, 0.826)
(a) (b)
(c) (d)
Figure 3. Probability of colonization of nest-sites by Arctic Peregrine Falcons in the Colville River Special Area, Alaska, related to
(a) nest height above the Colville River and (b) distance to the nearest neighbouring Arctic Peregrine Falcon nest, and probability of
local extinction of nest-sites by Arctic Peregrine Falcons related to (c) area of surrounding prey habitat and (d) nest-site productivity
from the previous year. Grey lines depict lower and upper 95% CIs.
© 2015 British Ornithologists’Union
Arctic Peregrine Falcon occupancy dynamics 7
Table 3. Model-averaged covariate coefficient estimates (and 95%) CIs from the best-approximating models (Table S4) from the
analysis examining factors related to cliff occupancy dynamics of Arctic Peregrine Falcons along the Colville River, Alaska, during
1981–2002. The response variable was y
kjt
, a binary variable denoting whether Arctic Peregrines were detected at cliff kduring sur-
vey jof year t. Covariates are defined in Table 1. Bold and italicized estimates indicate the covariate had strong and intermediate
support, respectively. n/a indicates the covariate was not included in the best-approximating models for that parameter.
Parameter
Covariate Initial occupancy probability Colonization probability Local extinction probability
intercept
a
0.755 (0.248, 1.76) 2.43 (3.84, 1.02) 3.13 (4.60, 1.66)
height
cliff,k
2.15 (0.608, 3.70) 0.703 (0.033, 1.37) 1.46 (2.17, 0.746)
waterarea
cliff,k
1.32 (0.125, 2.52) 0.279 (0.209, 0.768) 1.28 (1.94, 0.613)
productivity
cliff,k,t1
n/a n/a 1.27 (1.88, 0.653)
meltdate
t
n/a 0.621 (1.14, 0.099) n/a
precip
t
n/a n/a 0.290 (0.868, 0.289)
geology
k
=Qrb n/a 1.55 (0.195, 3.30) n/a
geology
k
=Qrc n/a 0.376 (1.35, 0.596) n/a
yearlog n/a 0.378 (0.070, 0.687) 0.333 (0.671, 0.004)
yearthreshold n/a 2.72 (0.287, 5.15) 2.20 (4.56, 0.151)
aspect
cliff,k
=north n/a n/a 0.613 (0.360, 1.59)
aspect
cliff,k
=northeast n/a n/a 0.944 (0.045, 1.93)
aspect
cliff,k
=northwest n/a n/a 0.127 (0.692, 0.946)
aspect
cliff,k
=south n/a n/a 0.761 (1.71, 0.187)
aspect
cliff,k
=southeast n/a n/a 0.429 (0.409, 1.27)
aspect
cliff,k
=southwest n/a n/a 1.01 (0.570, 2.59)
aspect
cliff,k
=west n/a n/a 0.172 (1.07, 1.41)
a
Intercept for c
kt
includes geology
k
= Qfp; intercept for e
kt
includes aspect
cliff,k
= east.
(a) (b)
(c) (d)
Figure 4. Probability of initial occupancy of cliffs by Arctic Peregrine Falcons in the Colville River Special Area, Alaska, related to (a)
nest height above the Colville River and (b) area of surrounding prey habitat, and probability of colonization of cliffs by Arctic Pere-
grine Falcons related to (c) nest height above the Colville River and (d) date of snowmelt. Grey lines depict lower and upper 95%
CIs.
© 2015 British Ornithologists’Union
8J. E. Bruggeman et al.
from the previous year and eastern aspects
(Table 3, Fig. 5). Local extinction was greater for
northeast and north aspects, and negatively associ-
ated with year as a logarithmic function, year as a
threshold function and south aspects with interme-
diate support. Detection probability varied
significantly by year for many years and was lower
during second surveys (survey
kt
coefficient
estimate =0.519, 95% CI =0.817, 0.221;
Fig. S1b). Estimates of annual occupancy probabil-
ity for all 74 cliffs during 1982–2002 ranged from
0.358 in 1983 to 0.712 in 2000
(mean =0.561 0.026 se; Fig. S2).
DISCUSSION
Selection of nest-sites by birds is often based on
cues across multiple spatial scales (Orians & Wit-
tenberger 1991, Luck 2002, Rauter et al. 2002).
Our results demonstrate the importance of rela-
tionships between multi-scale biotic and abiotic
factors and Arctic Peregrine nesting-season occu-
pancy dynamics, and account for imperfect detec-
tion through use of more than one survey during
the breeding season. Nest-site quality, height
above the Colville River, area of surrounding prey
habitat and temporal covariates received strong
support in our models at both nest-site and cliff
scales, whereas date of snowmelt was strongly sup-
ported in cliff-scale models. Our findings corrobo-
rate those of other studies that indicate that
conservation of bird habitats must account for
nest-site selection cues across multiple scales (e.g.
Saab 1999).
The negative relationship between local extinc-
tion and nest-site quality (i.e. productivity) sug-
gests that Arctic Peregrines having a successful
nest and greater number of young in one year are
more likely to occupy the same nest-site and cliff
in following years because returning results in
increased fitness (Newton 1979, Citta & Lindberg
2007). It is also possible that higher quality nest-
sites had higher productivity regardless of whether
Arctic Peregrines exhibited fidelity to the nest-site
or cliff. Positive relationships between occupancy
and site quality have been found for other bird
species (Matthysen 1990, L~
ohmus 2001, Marchesi
et al. 2002, Sergio & Newton 2003). Greater pro-
ductivity is also indicative of higher quality nesting
habitat, which is likely to be occupied earlier and
more frequently than lower quality habitat (Sergio
& Newton 2003).
The benefits of being an early migrant to breed-
ing territories include access to a larger selection of
higher quality nest-sites offering greater resource
availability and, possibly, reduced competition for
(a) (b)
(c)
Figure 5. Probability of local extinction of cliffs by Arctic Peregrine Falcons in the Colville River Special Area, Alaska, related to (a)
nest height above the Colville River, (b) area of surrounding prey habitat and (c) average nest-site productivity on the cliff during the
previous year. Grey lines depict lower and upper 95% CIs.
© 2015 British Ornithologists’Union
Arctic Peregrine Falcon occupancy dynamics 9
sites (Kokko 1999, Smith & Moore 2005). Factors
such as prey availability, protection from predators
and shelter from elements may all be instrumental
in affecting site choice (Mart
ınez et al. 2006). We
found height above the Colville River and area of
surrounding prey habitat, both associated with for-
aging efficiency and nestling survival, were factors
related to Arctic Peregrine occupancy dynamics.
Advantages of taller cliffs include better views of
potential predators and competitors, nearby prey,
and foraging habitat; providing an environment
where site occupants can quickly attain high veloc-
ities during attacks (Tucker 1998, Jenkins 2000);
and more difficult accessibility for ground-based
predators (Ratcliffe 1993). Jenkins (2000) showed
that Peregrines occupying taller cliffs achieved
greater hunting success, and that attacks initiated
from elevated perches on the cliff were more suc-
cessful than those started in flight. Peregrine occu-
pancy and nest success have been related to cliff
height, with nests located on taller cliffs being
more successful, having larger clutch and brood
sizes (Mearns & Newton 1988, Ratcliffe 1993,
Wightman & Fuller 2005, 2006). An adequate
food supply is essential for adults to attempt
breeding (Newton 1977, Martin 1987) and for sur-
vival of young, particularly during nestling and
fledgling stages (Korpim€
aki & Lagerstr€
om 1988,
Rohner & Hunter 1996). Cliffs surrounded by
greater area of prey habitat are likely to result in
less competition for resources among Arctic Pere-
grines, allowing cliffs to support more breeding
pairs.
Raptors selecting nest-sites located farther from
those of conspecifics experience less competition
for resources (Hakkarainen & Korpim€
aki 1996).
However, we found a negative relationship
between distance to the nearest occupied Arctic
Peregrine nest-site and colonization. Variability in
resource availability and types of cliff structures
along the Colville River is likely to explain our
observations, as nest-sites upriver were fewer in
number, had greater distances between sites and
often had only one site per cliff, suggesting a limi-
tation in the availability of quality sites and
resources. Arctic Peregrine nest-sites downriver
were located closer together, sometimes with mul-
tiple occupied sites per cliff, indicating sufficient
per-capita resources and cliffs with desirable physi-
cal attributes for nesting, even at higher nesting
densities. As the Arctic Peregrine population grew
in size during the 1980s and early 1990s, addi-
tional nest-sites were occupied on cliffs downriver
as opposed to cliffs upriver, suggesting that more
high-quality nest-sites existed downriver. It is also
possible that the presence of other nesting Arctic
Peregrines provides information about site quality
that may influence nest-site selection. Other stud-
ies have reported differing findings relating to spa-
tial relationships of nesting raptors (Olsen & Olsen
1988, Poole & Bromley 1998, Kr€
uger 2002).
Brambilla et al. (2006) found no influence of near-
est-neighbour distance on Peregrine cliff use, and
Wightman and Fuller (2005) found spacing among
occupied cliffs was related to annual variation in
Peregrine nest-site use.
Although Arctic Peregrines arriving early to the
CRSA may benefit from having access to higher
quality nest-sites, they may be limited due to late
snowmelt because Arctic Peregrines require a
snow-free substrate on which to nest. We found
that colonization of cliffs was negatively correlated
with date of snowmelt, suggesting that later spring
snowmelt inhibited nesting on some cliffs. Early-
arriving Arctic Peregrines to the CRSA first occupy
desirable nest-sites on snow-free cliffs, given suffi-
cient resources, and then search out snow-free
patches with suitable habitat on which to nest.
Earlier snowmelt provides a longer nesting season
and higher probability of a successful nest (Olsen
& Olsen 1989a, Bradley et al. 1997). Cliffs with
snow cover persisting later in the spring (e.g.
north-facing cliffs) are likely to be less desirable
for nesting to early-arriving Arctic Peregrines and
are less likely to be colonized and occupied in
future years.
Although our findings provide insights into
factors associated with nest-site occupancy of
high-latitude-nesting Peregrines, we note some
limitations and other considerations. First, the use-
fulness of GIS layers we used to derive covariates
was limited to their resolution, which may not
have adequately depicted finer scales at which
Peregrines may make final nest-site choices. Nest-
sites are usually located in areas of complex topog-
raphy, often with multiple aspects, and can be sit-
uated under overhanging structures that provide
protection from inclement weather (Grebence &
White 1989). Likewise, with the exception of the
MODIS/Terra-derived snow data, available climate
data were from point locations. Patterns in snow-
melt are highly variable on fine spatial scales and
depend on topography, aspect and other physical
characteristics.
© 2015 British Ornithologists’Union
10 J. E. Bruggeman et al.
Secondly, our use of 2001 land-cover data was
necessitated by a lack of older GIS data providing
coverage across the CRSA. It is possible that
changes in prey habitat occurred between 1981
and 2001, and that our covariates did not accu-
rately depict the area of prey habitat in the early
part of our study, although it is unlikely that the
area of prey habitat changed significantly through
the period of our study. We also could not docu-
ment annual variation in prey abundance through-
out our study.
Thirdly, because all nest-sites and cliffs included
in analyses were occupied at least once, inference
from our analyses is limited to these locations in
the study area. Our rationale for using this study
design results from two factors. Determining what
constituted a suitable nesting cliff or nest-site
before Arctic Peregrines occupied that cliff or
nest-site was difficult and subjective. In some
instances, Arctic Peregrines nested on surprisingly
small cliffs, the use of which would not have been
expected prior to occupancy. Therefore, only
occupied nest-sites and cliffs were documented
during surveys, and potential sites never occupied
were not identified. Also, the majority of cliffs
appearing to have suitable nest-sites within the
study area, based on observations during surveys
and evaluation of aerial imagery, were occupied at
least once, resulting in a small number of poten-
tially unoccupied cliffs. Furthermore, the possibil-
ity exists that external factors away from the
CRSA and not evaluated with our covariates had
an influence on occupancy dynamics. Recovery
from lingering DDT effects and climate and habi-
tat influences on wintering areas may have had a
role in increasing recruitment and immigration,
which would result in higher occupancy probabili-
ties.
Finally, we were logistically limited to conduct-
ing two surveys per year due to short nesting sea-
son duration, the size of the study area surveyed,
and the difficulty and expense of conducting sur-
veys in a remote area. More than two surveys may
have improved parameter and detection probabil-
ity estimates.
Conservation strategies for many long-lived spe-
cies with high site-fidelity generally treat all occu-
pied areas the same, regardless of site quality,
occupancy probability, history of productivity or
physical attributes. Our analyses suggest that for
Arctic Peregrines, and probably other species with
similar life-history strategies, individual sites could
be managed based on their attributes, with differ-
ent conservation strategies for different locations.
For Arctic Peregrines, nest-sites and cliffs with his-
torically higher productivity were occupied most
frequently and had lower local extinction probabil-
ity. In contrast, nest-sites and cliffs with histori-
cally low, or no, productivity were occupied less
frequently. These relationships suggest that from a
population perspective, protection of higher-qual-
ity nest-sites and cliffs is likely to have a more sub-
stantial effect on breeding Arctic Peregrines than if
the same protection were afforded to lower quality
sites, and current regulations could be relaxed
around unproductive nest-sites without popula-
tion-level consequences (e.g. Newton 1991, Sergio
& Newton 2003). Specifically, consideration could
be given to decreasing restrictions on potential
sources of human disturbance (camping, oil and
gas exploration, off-road foot travel) near nest-sites
and cliffs that have historically been unproductive
and/or not frequently occupied, while keeping
guidelines in place to minimize habitat loss and
fragmentation (U.S. Department of the Interior
Bureau of Land Management 2008). Historically,
higher occupancy rates existed downriver than
upriver, suggesting protection around downriver
nesting cliffs that also provided higher densities of
nesting sites would have the highest population-
level effects, presuming that survival rates and pro-
ductivity in more frequently occupied habitats are
high enough to result in stationary or increasing
population trends. However, some upriver nest-
sites had histories of relatively high occupancy
probability and productivity, indicating decisions
about what protection to afford nest-sites need to
be made at finer spatial scales. Protecting key nest-
ing locations, especially those on cliffs high above
the river drainage, surrounded by adequate prey
habitat, and with southern aspects associated with
early snowmelt will probably provide for contin-
ued occupancy by Arctic Peregrines in the CRSA
and other similar areas. Consideration of character-
istics of nest-sites and cliffs associated with high
occupancy, and not just productivity, is important
when making decisions about protection of Pere-
grines. Identifying these landscape characteristics
may also be useful in predicting and mapping the
probability of nest-site use in areas other than
known nesting cliffs.
Our study provides an example of how dynamic
occupancy models can be applied to a species for
which nesting habitat quality and availability are
© 2015 British Ornithologists’Union
Arctic Peregrine Falcon occupancy dynamics 11
relatively stable over the span of multiple decades,
while also assessing the importance of annual cli-
mate variability. Whereas initial occupancy proba-
bility can be related to time-independent habitat
and landscape factors, the influence of time-depen-
dent and time-independent factors on colonization
and local extinction probabilities can be evaluated.
Furthermore, our study illustrates how historical
datasets with a minimum of two annual surveys
during the breeding season can be used in dynamic
occupancy models, which are ideal to help address
conservation and management issues and inform
decision making (Martin et al. 2009).
Funding for this study was provided by the U.S. Fish
and Wildlife Service and Bureau of Land Management
in Fairbanks, Alaska. We are grateful to T. Cade and
C. White for their tremendous contributions to the
study and conservation of raptors in Alaska, including
their seminal work on raptor ecology along the Colville
River in the 1950s and 1960s. S. Ambrose led Pere-
grine-monitoring efforts in Alaska for many years and
we appreciate his leadership and support. We thank C.
Hamfler for providing GIS data and support, J. Brown,
T. Katzner, Z. Wallace and one anonymous reviewer for
review of the manuscript, and 32 colleagues who pro-
vided insight and helped collect the data used in this
paper. B. Dittrick, P. Schempf and J. Silva led survey
efforts in 1983, 1984 and 1986, respectively, and we
thank them for use of their observations. Use of trade
names does not imply endorsement by the U.S. Federal
Government, University of Minnesota or Oregon State
University.
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Received 25 July 2014;
revision accepted 2 September 2015.
Associate Editors: Jose Antonio Sanchez-Zapata and Jen Smart.
SUPPORTING INFORMATION
Additional Supporting Information may be found
in the online version of this article:
Data S1. Descriptions of the stepwise modelling
procedures for our nest-site and cliff occupancy
analyses.
Table S1. Predictions for covariates evaluated in
analyses examining factors related to occupancy
dynamics of Arctic Peregrine Falcons on nest-sites
and cliffs.
Table S2. Range, mean, se and sample size for
numerical covariates used in analyses examining
nest-site and cliff occupancy dynamics of Arctic
Peregrine Falcons.
Table S3. Complete list of model results from
the analysis examining factors related to nest-site
occupancy dynamics of Arctic Peregrine Falcons.
Table S4. Complete list of model results from
the analysis examining factors related to cliff occu-
pancy dynamics of Arctic Peregrine Falcons.
Figure S1. Temporal trends in detection proba-
bility of nesting Arctic Peregrine Falcons for two
surveys per summer of (a) individual nest-sites and
(b) cliffs.
Figure S2. Temporal trends in the probability
of Arctic Peregrine Falcon occupancy of individual
nest-sites and cliffs.
© 2015 British Ornithologists’Union
14 J. E. Bruggeman et al.
