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Modelling population dynamics in presence of
hybridization
Nina Santostasi
To cite this version:
Nina Santostasi. Modelling population dynamics in presence of hybridization. Agricultural sci-ences. Université Montpellier; Università degli studi La Sapienza (Rome), 2020. English. �NNT : 2020MONTG017�. �tel-03144074�
SAPIENZA
Università di Roma
Facoltà di Scienze Matematiche Fisiche e Naturali
PH. D. IN ENVIRONMENTAL AND EVOLUTIONARY BIOLOGY
Cycle: XXII
(A.Y. 2019/2020)
Modelling population dynamics in presence of hybridization
Ph. D. Student
Nina Luisa Santostasi
Supervisors
Coordinator
Prof. Gabriella Pasqua
Prof. Paolo Ciucci
Dept. Biology and Biotechnologies,
THÈSE POUR OBTENIR LE GRADE DE DOCTEUR
DE L’UNIVERSITÉ DE MONTPELLIER
En Ecologie et Biodiversité
École doctorale GAIA
Unité de recherche UMR 5175- CEFE- Centre d’Ecologie Fonctionnelle et Evolutive
En partenariat international avec Sapienza Université de Rome, Italie
Présentée par Nina Luisa Santostasi
Fèvrier 2020
Sous la direction de Olivier Gimenez et Paolo Ciucci
Modélisation de la dynamique des populations en présence
d'hybridation
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INDEX
1. GENERAL INTRODUCTION……… 2. CHAPTER 1: Development of a multievent capture–recapture model to estimateWKH
prevalence of admixed individuals in wildlife populationV...………...…………..2 3. APPENDIX CHAPTER 1……….………………3 4. CHAPTER 2: EstimatiQJ the prevalence of admixed wolf x dog individuals in a study area in the northern Apennines, Italy……….………..5 5. APPENDIX CHAPTER 2.……… 6. CHAPTER 3: Development of a population-based modelling approach to project hybridization dynamics………...……19 7. APPENDIX CHAPTER 3……….………..……1 8. CHAPTER 4: Development of an individual-based model to evaluate the effect of different hybridization management strategies for the wolf x dog case study………...….1 9. APPENDIX CHAPTER 4……….………….………..……2
1. GENERAL INTRODUCTION
1
1.1 Natural and anthropogenic hybridization
2
Hybridization, the interbreeding of individuals from genetically distinct populations, regardless of 3
their taxonomic status (Allendorf et al. 2001) is acknowledged to be a relatively common 4
evolutionary process both in the plant and animal kingdoms (Hewitt, 1988; Olden et al. 2004; 5
Grabenstein & Taylor 2018). Hybridization is mainly observed between otherwise allopatric taxa 6
that come into contact due to natural (natural hybridization) or anthropogenic causes (anthropogenic 7
hybridization, e.g., changes in the abundance and distribution of species, the removal of barriers 8
that cause isolated or restricted species to expand, and/or the uncontrolled diffusion of domestic 9
species). Todesco et al. (2016) performed a literature review of hybridization studies to identify the 10
ecological, evolutionary, and genetic factors that critically affect extinction risk through 11
hybridization. They found that 72% of studies regarding anthropogenic hybridization reported an 12
extinction threat and among those the most common anthropogenic causes of hybridization were 13
husbandry or agriculture (55% of the studies), invasive species (54%), and habitat disturbance 14
(36%). Most of the studies dealt with hybridization in plants, followed by fishes, birds, and 15
mammals. Extinction risk was more common in hybridizing vertebrates than plants and appeared to 16
be driven by fish (85% of the studies) and birds species (79% of the studies). 17
Anthropogenic hybridization is therefore considered as an increasing and significant threat to 18
biodiversity (Rhymer & Simberloff 1996; Crispo et al. 2011) that has the potential of driving rare 19
taxa to genomic extinction (the loss of combinations of genes and genotypes that have a unique 20
hybridization can cause extinction through genetic swamping (where the rare form is replaced by 27
hybrids; Allendorf et al. 2001). Following genomic extinction, the result is frequently a ‘hybrid 28
swarm’ in which all the individuals composing a population are hybrids. 29
30
1.2 When hybridization is a threat: importance of quantifying the prevalence of admixed individuals
31
in and its dynamics
32
As with any conservation threat, to evaluate potential management actions, it is fundamental to: 1) 33
understand if hybridization poses a threat to the viability of a population that requires human 34
intervention, 2) identify possible management actions and evaluate their effectiveness in an 35
adaptive management loop (Williams et al. 2011). For the first point, Allendorf et al. (2001) 36
proposed a classification framework to assess the severity of the hybridization threat. They divided 37
anthropogenic hybridization cases in different types based mainly on two criteria: the fitness and 38
relative abundance of admixed individuals (i.e., prevalence of admixed individuals). In the first 39
anthropogenic hybridization type ("hybridization without introgression"), first-generation hybrids 40
are sterile and the main threat for parental populations is the waste of reproductive effort 41
(demographic swamping). In the second type ("widespread introgression"), hybrids are fertile but 42
the parental populations are still prevalent and well distinguished. In the third type ("complete 43
admixture"), widespread introgression can evolve into a situation in which only the admixed 44
individuals remain (genetic swamping). Understanding the type of hybridization that is occuring is 45
therefore fundamental to assess the threat posed by anthropogenic hybridization on the viability of 46
the parental population and timely elaborate management strategies (Allendorf et al. 2001; Bohling 47
2016). To understand the hybridization type we need to quantify the proportion of admixed 48
individuals in a population at a given time (hereafter prevalence) and understand if such quantity is 49
predicted to increase toward complete admixture. 50
For the second point, depending on the hybridization type, a variety of management actions 51
hybrids to the management of the human disturbances that facilitatHG hybridization in the first 53
place (Allendorf et al. 2001; Bohling 2016). 54
55
1.2.1 Methodological challenges and solutions to estimate the prevalence of admixed
56
individuals
57
The relative abundance (prevalence) of different categories of individuals within a population is an 58
essential piece of information to understand processes in ecology, evolution, and conservation. For 59
example, the prevalence of infected individuals is critical to understand disease dynamics (Jennelle, 60
et al. 2007) and the prevalence of key demographic categories (e.g., mature females) is needed to 61
predict the viability of populations (Caswell 2000). Estimating the prevalence of different 62
population segments in wildlife populations is not trivial, therefore naive prevalence (the proportion 63
of individuals of a given class in the sample) is often used as a proxy (Jennelle et al. 2007). 64
However, this approach overlooks two main sources of bias: first, imperfect and/or heterogeneous 65
probability of detection leads to biased abundance and prevalence estimates when it is ignored 66
(Jennelle et al. 2007; Cubaynes et al. 2010), second, uncertainty in the classification of individuals 67
is common when individuals are assigned to a specific category based on clues (i.e., the assignment 68
of individuals to the category admixed and parental based on a limited number of genetic markers; 69
Vähä & Primmer 2006). 70
Reliable estimates of prevalence can be obtained by correcting field counts by the proportion 71
of undetected individuals (i.e., the ratio between the number of observed individuals and the 72
process in the model structure (Pradel 2005). Multievent models have been used to estimate a 79
variety of population parameters in the presence of uncertainty in classification (e.g., rates of entry 80
and exit from disease states: Conn & Cooch 2009; probability of skipping reproduction: Sanz-81
Aguilar et al. 2011, and the probability of survival of different age classes: Gervasi et al. 2017). 82
However, multievent models have never been used to estimate the abundance and prevalence of 83
different classes of individuals in a population. 84
85
1.2.2 Methods for projecting hybridization dynamics
86
Once hybridization has been estimated within a period of biological relevance (i.e., reproductive or 87
generational), it is important to understand if such quantity is predicted to increase towards 88
complete admixture. Moreover, if hybridization is recognized as a legitimate threat, the type and 89
intensity of management action need to be chosen and their outcome need to be evaluated 90
(Allendorf et al. 2001; Bohling 2016). 91
Population projection models are widely used in other contexts (e.g., harvest modelling 92
Sutherland 2001) to simulate population dynamics under different biological/evolutionary scenarios 93
and provide management recommendations (Cross & Beissinger 2001; Hradsky et al. 2019) but 94
their application to assess hybridization as a threat are few, though recently increasing (e.g., Nathan 95
et al. 2016). The first attempts to model hybridization-extinction dynamics had a genetic focus and 96
were based on changes in allelic frequencies at one or more loci (Huxel 1999; Ferdy & Austerlitz 97
2002). On the other hand, ecological models explicitly examine the effects of life-history traits (e.g., 98
survival and reproductive rates) on the hybridization outcome. Within this approach, two types of 99
models have been used to model hybridization dynamics (Hall & Ayres 2008): 1) individual-based 100
models that simulate the contribution of each individual to the hybridization dynamics of the entire 101
population (e.g., Thompson et al. 2003; Hooftman et al. 2007), and 2) population-based models that 102
can be used when only the mean fitness parameters of the main demographic stages are available 103
hybridization in plant species (Hall & Ayres 2008; Todesco et al. 2016). However, few studies used 105
individual-based models (Fredrickson & Hedrick 2006; Nathan et al. 2019) to simulate 106
hybridization dynamics in animal species. 107
108
1.3 General scope of the Ph.D. project
109
The general scope of my Ph.D. was to develop models for the assessment and management of 110
extinction risk due to anthropogenic hybridization. To provide a practical demonstration of the use 111
of the developed models we used them on an emblematic anthropogenic hybridization case study: 112
the hybridization between wolves (Canis lupus) and dogs (Canis lupus familiaris) in human 113
dominated landscapes. 114
115
1.3.1 Wolves x dog hybridization in Europe
116
Wolves and dogs are interfertile and the first-generation hybrids can backcross with both parental 117
sub-species, generating gene flow between the two gene pools (Vilà & Wayne 1999). Hybridization 118
between wolves and dogs occurred repeatedly since dog domestication (15-10.000 years BP; Larson 119
et al. 2012; Pilot et al. 2018), but more recent (i.e., up to 2 generations since admixture) 120
introgressive hybridization has been detected in various wolf populations in Eurasia (Galaverni et 121
al. 2017; Pacheco et al. 2017; Pilot et al. 2018; Dufresnes et al. 2019). In Europe, the expansion of 122
recovering wolf populations through human-dominated landscapes (Chapron et al. 2014), where 123
free-ranging dogs have since long become the most abundant carnivore (Ritchie et al. 2014) creates 124
genomic integrity of European wolf population is one the conservation priorities for wolves in 131
Europe (Hindrickson et al. 2017). 132
Studies on wolf-dog hybridization in several European countries have been mostly based on 133
non-invasive genetic sampling (reviewed in Dufresnses et al. 2019) and found revealed relatively 134
low proportions RIDGPL[HGLQGLYLGXDOVLQWKHFROOHFWHGVDPSOHVDQGLQ:HVWHUQDQG 135
Eastern Europe, respectively). However, these results may be flawed due to two main reasons. First 136
many of these samples have been collected opportunistically and at a coarse spatial (i.e., national) 137
and temporal (i.e., decades) scales (Dufresnes et al. 2019), whereas hybridization occurs at the local 138
scale and within one generation time. In support to that we highlight that, although large scale 139
assessments failed to detect high prevalence of admixture (Randi & Lucchini, 2002; Verardi et al. 140
2006; Lorenzini et al. 2014) more recent studies, based on intensive sampling at the local scale 141
(Caniglia et al. 2013; Bassi et al. 2017; Salvatori et al. 2019; this study), revealed higher admixture 142
rates even if still based on naLve prevalence quantifications. 143
Second, naive prevalence quantifications may suffer from both the heterogeneous 144
detectability of parental and admixed individuals, and the uncertainty in their classification. The 145
systematic monitoring of prevalence in wild populations relies on non-invasive samples (e.g., hairs 146
or scats), therefore the relatively poor-quality DNA extracted from such samples only allows for the 147
amplification of a relatively low number of diagnostic loci (Randi et al. 2014), limiting the power to 148
discriminate between parental individuals and later (>2) generation backcrosses (Vähä & Primmer 149
2006). This generates uncertainty over the classification of some DOOHJHGO\DGPL[HGJHQRW\SHV 150
3rd generation backcrosses; Vähä & Primmer 2006), that are generally arbitrarily assigned to wolves 151
(e.g., Pacheco et al. 2017; Dufrenses et al. 2019), a practice that avoids Type 1 error (i.e., 152
misclassifying wolves as admixed individuals) but not necessarily Type 2 error (i.e., misclassifying 153
admixed individuals as wolves). 154
Based on the low proportions of admixed individuals detected in Western European studies 155
dog hybridization is currently rare and where it occurs, it most likely takes place in the peripheral 157
portion of the wolf distribution (Lorenzini et al. 2014) and/or during phases of range expansion 158
(Galaverni et al. 2017; Kusak et al. 2018). The second is that introgression of dog genes into wolf 159
populations is expected to be buffered by behavioral and selective constraints (e.g., the unsuccessful 160
integration of pregnant females in the natal packs, the reduced survival of first generation hybrid 161
litters due to limited paternal care, the lower success of admixed individuals in territorial or 162
predatory interactions; Vilà & Wayne 1999), and/or by the dilution of dog genes through 163
backcrossing into the parental wolf populations (Verardi et al. 2006). Based on these assumptions 164
and possibly due to the inherent biological and social complexity characterizing control of wolf-dog 165
hybridization (Donfrancesco et al. 2019), active management has lagged behind in Europe, 166
notwithstanding formal guidelines and recommendations provided by the European Union 167
(Salvatori & Ciucci 2018; Salvatori et al. 2019). 168
169
1.3.2 Wolf x dog hybridization as a threat
170
Although there was consensus among a panel of 42 wolf x dog hybridization experts across the 171
world regarding the fact that anthropogenic hybridization should be mitigated (Donfrancesco et al. 172
2019), clear evidence has not yet been found that the introgression of dog genes is a real 173
conservation issue. 174
Dogs diverged from the grey wolf Canis lupus between 11,000 and 35,000 years ago (Freedman & 175
Wayne, 2017). However, Larson et al. (2012) suggested that the current gene pool of most dog 176
levels, changed concentrations of several neurotransmitters, prolongations in juvenile behavior, and 183
reductions in both total brain size and of particular brain regions (Wilkins et al. 2014). For dogs 184
several behavioural traits differentiated them from wild canids (Miklosi 2015) and the genetic basis 185
of these traits is being unveiled (vonHoldt et al. 2017). The consequence of the LQWURJUHVVLRQRI 186
such traits in a wild wolf population have not yet beHQ addressed. 187
The only case where some of the long term consequences of the introgression of dog alleles 188
in wild wolf population gene pool have been explored is the introgression (and following positive 189
selection) of the melanistic mutation at the K-locus in the wolf gene pool in North American wolves 190
(Anderson et al. 2009). This mutation determines the black color in dogs (Candille et al. 2007) 191
and was likely introduced into North American wolves by ancient hybridization with dogs (12-192
14,000 years ago; Anderson et al. 2009). Coulson et al. (2011) found that gray wolves had slightly 193
lower survival, recruitment, generation length, and lifetime reproductive success than black 194
heterozygotes for the melanistic mutation. Coulson et al. (2011) also observed that black 195
homozygotes had lower survival, recruitment, generation length, and lifetime reproductive success 196
than black heterozygotes and gray wolves. Stahler et al. (2013) carried a detailed analysis of the 197
life-history traits of the population for both different colors and sexes and found that gray females 198
had more surviving pups than black females, the latter of which were nearly all heterozygotes. It is 199
therefore possible that the beta-defensin gene that determines black color in wolves might have 200
pleiotropic effects on disease resistance or other immunologically related traits (Coulson et al. 201
2011) and result in fitness tradeoffs. 202
Although hybridization with dogs is not only a recent phenomenon and, in this particular case, it 203
seems to have led to potential adaptive variation (together with possible pleiotropic effects), it is 204
reasonable to hypothesize that the forces that shaped introgression of domesticated alleles in North 205
American wild wolf populations 12,000 years ago are much different than the forces that would act 206
on introgressed dog alleles in the Anthropocene. In addition to that, the relative abundance of 207
abundant carnivore in the world (Ritchie et al. 2014) while wolves faced almost eradication 209
(Chapron et al. 2014). As a result of conservation efforts, gray wolves are currently re-colonising 210
parts of their former range in Western Europe across human-dominated landscapes (Chapron et al. 211
2014). Although gray wolves are able to survive and reproduce in anthropogenic habitats, the 212
survival rates and the causes of mortality in these systems will likely differ from those in less 213
human-dominated settings. These habitats are characterized, among other things, by high densities 214
RIanthropogenic foods (e.g., livestock, human food waste) that has been OLQNHGWRFKDQJHVLQ dietary 215
habits of predators, which may OHDGWR JHQHWLFbehavioural DQGGHPRJUDSKLFchanges (Newsome et 216
al. 2015). In this context the interaction RIDQWKURSRJHQLFVHOHFWLRQDQG introgressed GRPHVWLFDWHG 217
DOOHOHVPD\FRQWULEXWHWRWKHchanges in ecological niche (and role) and evolutionary diversification. 218
7KHSRVVLEOHRXWFRPHVRIsuch process may lead to the evolution of a new dog-like wolf ecotype, or to the 219
JUDGXDOreplacement of wolves by admixed individuals in human-dominated landscapes (genetic 220
swamping). 221
Given these considerations and following a precautionary approach wolf x dog hybridization is 222
largely perceived as a threat by experts of the field (Donfrancesco et al. 2019), a vision that is 223
shared by the author of this manuscript. 224
225
1.3.3 Management of wolf x dog hybridization
226
The management of anthropogenic hybridization involves three types of actions (Donfrancesco et 227
al. 2019): preventive (e.g., community engagement and education to decrease the number of free-228
proactive measures are generally enforceable through the national and European legislation, agreed 235
upon and supported by experts and socially more acceptable. On the other hand reactive measures 236
are controversial due to the not-defined legal status of hybrids, the lack of consensus within both the 237
scientific community and the general public (Lorenzini et al. 2014; Donfrancesco et al. 2019). The 238
effectiveness of reactive management has also been questioned by several authors (Lorenzini et al. 239
2014, Pacheco et al. 2017). 240
It is difficult if not impossible to empirically assess the effectiveness of reactive 241
hybridization management strategies due to the general lack of long-term time data series and the 242
need to implement management timely. Demographic simulation models can help exploring 243
complex ecological and evolutionary processes that are not easily empirically measured (Nathan et 244
al. 2019) and can be instrumental to inform decision-making in a context of uncertainty (e.g., 245
Gervasi & Ciucci 2018). To our knowledge, while population projections have been used to test the 246
effectiveness of the sterilization of admixed breeders is in the intensively monitored red wolf (Canis 247
rufus) x coyote (Canis latrans) system in North Carolina (Fredrickson & Hedrick 2006), they have
248
never been used to compare management strategies in the context of wolf x dog hybridization and 249
in general rarely for animal species (but see Nathan et al. 2019). 250
251
1.4 Structure and specific objectives of the Ph.D manuscript
252
This manuscript consists in four chapters, three of which (Chapter 1, 3 and 4) aiming at developing 253
methodological frameworks to quantify the prevalence of admixed individuals and its dynamics. 254
The second chapter is entirely dedicated to the application of the estimation model developed in 255
Chapter 1 to the case study on wolf x dog hybridization in the Northern Apennines, Italy. 256
257
1.4.1 Chapter 1. Development of a prevalence multievent capture–recapture model to
258
estimate prevalence of admixed individuals in wildlife populations
This chapter has been published: Santostasi, N.L., Ciucci, P., Caniglia, R., Fabbri, E., Molinari, L., 260
Reggioni, W., Gimenez, O. (2019). Use of hidden Markov capture–recapture models to estimate 261
abundance in the presence of uncertainty: Application to the estimation of prevalence of hybrids in 262
animal populations. Ecology and Evolution 9, 744-755. 263
In this chapter we: 1) developed a multievent capture–recapture model to estimate 264
prevalence in free-ranging populations accounting for imperfect detectability and uncertainty in 265
individual's classification, 2) carried out a simulation study to i) evaluate model performance, ii) 266
compare it to naive quantifications of prevalence and iii) assess the accuracy of model-based 267
estimates of prevalence under different sampling scenarios. The main results from this chapter were 268
that i) the prevalence of hybrids could be estimated while accounting for both detectability and 269
classification uncertainty ii) model-based prevalence consistently had better performance than 270
naive prevalence in the presence of differential detectability and assignment probability 271
and was unbiased for sampling scenarios with high detectability. Our results underline the 272
importance of a model-based approach to obtain unbiased estimates of prevalence of different 273
population segments. 274
275
1.4.2 Chapter 2. EstimatiQJ the prevalence of admixed wold x dog individuals in a study
276
area in the northern Apennines, Italy
277
This chapter is currently submitted: Santostasi, N.L., Gimenez, O., Caniglia, R., Fabbri, E., 278
illustrate the implications of the results for wolf conservation and for the management of wolf x dog 286
hybridization in human-dominated landscapes. In particular, by taking into account imperfect 287
detectability and the uncertainty associated with the assignment of backcrossed admixed 288
individuals, we estimated 64-78% recent hybrids occurring in 6 out of the 7 surveyed packs. 289
Ancestry analysis and genealogy reconstructions also confirmed multi-generational introgression 290
and indicated that some admixed packs had one or both breeders of recent admixture. Our findings 291
underline that in human-modified landscapes wolf-dog hybridization may raise to unexpected levels 292
if left unmanaged, and that reproductive barriers or dilution of dog genes through backcrossing 293
should not be expected, per se, to prevent occurrence and the spread of introgression. 294
295
1.4.3 Chapter 3. Development of a population-based modelling approach to project
296
hybridization dynamics
297
This chapter is currently accepted pending minor revisions: Santostasi, N.L., Ciucci, P., Bearzi, G., 298
Bonizzoni, S., Gimenez, O.(In press). Assessing the dynamics of hybridization through a matrix 299
modelling approach. Ecological Modelling. 300
In this chapter we present a new matrix population model to project population dynamics of 301
animal populations in presence of hybridization. We apply the model to two real-world case studies 302
of terrestrial (wolf x dog) and marine mammal species (common dolphin Delphinus delphis x 303
striped dolphin Stenella coeruleoalba). Specifically, we investigate 1) the possible outcomes of 304
wolf x dog hybridization events for an expanding wolf population in Italy, under different 305
reproductive isolation scenarios, 2) the genomic extinction probability of the two interbreeding 306
dolphin species within a semi-enclosed gulf in Greece, under different hybrids’ fitness scenarios, 3) 307
the sensitivity of the probability of genomic extinction to the main demographic parameters in the 308
two case studies. In particular our projections highlighted that i) hybridization leads to genomic 309
extinction in the absence of reproductive isolation, ii) rare or depleted species are particularly 310
parameters of parental species, iiii) maintaining healthy and abundant populations prevents genomic 312
extinction. 313
314
1.4.4 Chapter 4. Development of an individual-based model to evaluate the effect of
315
different management strategies for wolf x dog hybridization
316
In this chapter we built a detailed individual based model describing the life cycle of the 317
gray wolf by contemplating social dynamics traits linked to hybridization rates. We applied this 318
model to investigate the hybridization dynamics of wolves in a study population the Northern 319
Apennines, Italy, to evaluate the effectiveness of different management scenarios aimed to reduce 320
the abundance of admixed individuals during a ten-generation time. We showed that in presence of 321
frequent immigration of admixed individuals any management action proved ineffective. In 322
presence of immigration by pure wolves all management actions produced a decrease in prevalence, 323
although their relative effectiveness changed depending on the mating choice scenario. In all the 324
simulated scenarios, the impact of hybridization is predicted to extend at broad scales as large 325
numbers of admixed dispersers are produced. Moreover, we identified demographic and social 326
processes that need to be further investigated to more accurately project the outcomes of 327 management alternatives. 328 329 330 LITERATURE CITED 331
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Պ 11;r|;7ĹƔ";r|;l0;uƑƏƐѶ DOI: 10.1002/ece3.4819O R I G I N A L R E S E A R C H
Use of hidden Markov capture–recapture models to estimate
abundance in the presence of uncertainty: Application to the
estimation of prevalence of hybrids in animal populations
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$_; u;Ѵ-|b; -0m7-m1; Őru;-Ѵ;m1;ő o= 7b==;u;m| rorѴ-|bom v;]Ŋ ments is a fundamental piece of information to understand proŊ 1;vv;v bm ;1oѴo]ķ ;oѴ|bomķ -m7 1omv;u-|bomĺ ou ;-lrѴ;ķ |_; prevalence of infected individuals is critical to understand the mechŊ -mbvlv7ubbm]7bv;-v;7m-lb1vŐ;mm;ѴѴ;ķoo1_ķomuoķş";m-uķ ƑƏƏƕĸou;moŊ$ouu;vķ)oѴ=;ķ"-bѴѴ;ķş-u-0;7ķƑƏƐѵőĸ|_;ru;-Ŋ Ѵ;m1;o=h;7;lo]u-r_b11-|;]oub;vŐ;ĺ]ĺķl-|u;=;l-Ѵ;vőbvm;;7;7 |o -vv;vv |_; b-0bѴb| o= ;m7-m];u;7 rorѴ-|bomv Ő-v;ѴѴķ ƑƏƏƏő -m7_;m_0ub7b-|bomu;ru;v;m|v-|_u;-|ķ|_;ru;-Ѵ;m1;o=-7Ŋ lb;7bm7bb7-Ѵvbvm;;7;7|o;-Ѵ-|;|_;-rruorub-|;l-m-];l;m| or|bomŐѴѴ;m7ou=ķ;-uķ"ru;ѴѴķş);m0u]ķƑƏƏƐőĺ
o;;uķ;v|bl-|bm]ru;-Ѵ;m1;=oubѴ7Ѵb=;rorѴ-|bomvbv1_-ѴŊ lenging and the raw percentage of individuals of a class in the sample Őm-b; ru;-Ѵ;m1;ő bv o=|;m v;7 -v - ruo Ő;mm;ѴѴ; ;|-Ѵĺķ ƑƏƏƕőĺ o;;uķ|_bv-rruo-1_o;uѴoohv|ol-bmvou1;vo=0b-vĺ buv|ķ imperfect and/or heterogeneous detection leads to biased abunŊ 7-m1;;v|bl-|;v_;mb|bvb]mou;7Ő0-m;v;|-ѴĺķƑƏƐƏĸ;mm;ѴѴ; ;|-ѴĺķƑƏƏƕőĺ";1om7ķm1;u|-bm|bm|_;1Ѵ-vvb=b1-|bomo=bm7bb7-Ѵv Ő;ĺ]ĺķ 7bv;-v;7ņ_;-Ѵ|_ķ 0u;;7;uņmom0u;;7;uķ l-Ѵ;ņ=;l-Ѵ;ő bv 1olŊ mon in wildlife population studies where individuals are assigned to -vr;1b=b1v|-|v0-v;7omblr;u=;1|1Ѵ;vĺ-lrѴ;vbm1Ѵ7;7;|;uŊ lbmbm]v;ou0u;;7bm]v|-|v0-v;7om|_;0;_-bouo=bm7bb7-Ѵv Ő;mo-u|ķu-7;ѴķşuoķƑƏƐƑőou;v|-0Ѵbv_bm]_;-Ѵ|_v|-|v=uol |_; o0v;u-|bom o= o|;u vlr|olv omѴ Őomm ş oo1_ķ ƑƏƏƖőĺ mo|_;uѴ;vv;rѴou;70|bm|ub]bm]vb|-|bombv-vvb]mbm]bm7bb7-Ѵv |o];m;|b11Ѵ-vv;vŐv0rorѴ-|bomvő0-v;7om-Ѵblb|;7ml0;uo=];Ŋ m;|b1l-uh;uvŐ(࢜_࢜şubll;uķƑƏƏѵőĺ !;Ѵb-0Ѵ; ;v|bl-|;v o= bѴ7Ѵb=; -0m7-m1; 1-m 0; o0|-bm;7 0 1ouu;1|bm]=b;Ѵ71om|v0|_;ruorou|bomo=m7;|;1|;7bm7bb7-Ѵv Őbĺ;ĺķ|_;u-|bo0;|;;m|_;ml0;uo=o0v;u;7bm7bb7-Ѵv-m7|_; ruo0-0bѴb|o=7;|;1|bomĸb1_oѴvķƐƖƖƑőĺ$_;ruo0-0bѴb|o=7;|;1|bom bvv-ѴѴ;v|bl-|;70vbm]1-r|u;ŋu;1-r|u;lo7;ѴvŐ!ő=uol- v-lrѴ;o=bm7bb7-Ѵ;m1om|;u_bv|oub;vŐ|bvķum_-lķ)_b|;ķş m7;uvomķ ƐƖƕѶőĺ m r-u|b1Ѵ-uķ lѴ|bv|-|; ! lo7;Ѵv ;v|bl-|; |_; ruo0-0bѴb| o= 7;|;1|bom =ou 7b==;u;m| 1Ѵ-vv;v o= bm7bb7-Ѵv 0 -vŊ vb]mbm]bm7bb7-Ѵv|ov|-|b1ou7m-lb1v|-|;vĺo;;uķlѴ|bv|-|; CR models assume the correct assignment of all individuals to their v|-|;Ő;0u;|omķum_-lķѴo0;u|ķşm7;uvomķƐƖƖƑőĺѴ|b;;m| lo7;Ѵvu;Ѵ-|_bv-vvlr|bom0-1hmoѴ;7]bm]|_;m1;u|-bm|o= |_; o0v;u-|bom ruo1;vv bm |_; lo7;Ѵ v|u1|u; Őu-7;Ѵķ ƑƏƏƔőĺ m |_;v;lo7;Ѵvķ-_b77;m0boѴo]b1-Ѵruo1;vvŐ;ĺ]ĺķvub-Ѵou7bvr;uv-Ѵő bvlo7;Ѵ;7-v--uho1_-bmo=v|-|;vŐu-7;ѴķƑƏƏƔőĺ$_;o0v;u-Ŋ |bomruo1;vvŐ|_;7-|-ő-ubv;v=uol|_;m7;uѴbm]v|-|;v|_uo]_|_; ruo0-0bѴb|o=7;|;1|bomĺ$obm1Ѵ7;m1;u|-bm|bmv|-|;-vvb]ml;m|ķ the observation process is further split into two steps: detection -m7v|-|;-vvb]ml;m|1om7b|bom-Ѵom7;|;1|bomŐbl;m;ķ;0u;|omķ -bѴѴ-u7ķ_ot;|ķşu-7;ѴķƑƏƐƑĸu-7;ѴķƑƏƏƔőĺ$_bv=oulѴ-|bom bm1Ѵ7;v-ruo0-0bѴb|o=-vvb]ml;m|Ő0;vb7;v|_;ruo0-0bѴb|o=7;Ŋ |;1|bom-m7|_;ruo0-0bѴb|b;v-vvo1b-|;7b|_|_;0boѴo]b1-Ѵruo1;vvőķ -ѴѴobm]=ou|_;bm1Ѵvbomo=bm7bb7-Ѵv1Ѵ-vvb=b;7b|_m1;u|-bm| Ѵ|b;;m|lo7;Ѵv_-;0;;mv;7|o;v|bl-|;--ub;|o=rorŊ Ѵ-|bomr-u-l;|;uvbm|_;ru;v;m1;o=m1;u|-bm|bmv|-|;-vvb]ml;m|ĺ -lrѴ;vo=|_-|bm1Ѵ7;|_;u-|;vo=;m|u-m7;b|=uol7bv;-v;v|-|;v Őommşoo1_ķƑƏƏƖőķ|_;ruo0-0bѴb|o=vhbrrbm]u;ruo71|bomŐ"-mŊ ]bѴ-u ;|-Ѵĺķ ƑƏƐƐőķ -m7 |_; ruo0-0bѴb| o= vub-Ѵ o= 7b==;u;m| -]; 1Ѵ-vv;vŐ;u-vb;|-ѴĺķƑƏƐƕőĺo;;uķlѴ|b;;m|lo7;Ѵv_-;m;;u been used to estimate the abundance of individuals in different states 0;1-v;|_;ml;u-|ouo=|_;-0m7-m1;;v|bl-|ouŐ|_;ml0;uo= o0v;u;7bm7bb7-Ѵvőbv1om|-lbm-|;70m1;u|-bmo0v;u-|bomvĺ ;u;ķ;7;;Ѵor-1-r|u;ŋu;1-r|u;-rruo-1_|o;v|bl-|;|_; ru;-Ѵ;m1;o=-7lb;7bm7bb7-ѴvŐ_;u;-=|;uľ_0ub7vĿőbm-rorѴ-|bom _bѴ;vblѴ|-m;ovѴ-11om|bm]=ou0o|_blr;u=;1|7;|;1|bom-m71Ѵ-vŊ vb=b1-|bomm1;u|-bm|ĺ"r;1b=b1-ѴѴķ;v_o_o|ov;|_;lѴ|b;;m| CR framework to estimate abundance of individuals in different states Őbĺ;ĺķ ľ-u;m|-ѴķĿ ľ0ub7ķĿ ľ ;-7Ŀő bm |_; ru;v;m1; o= m1;u|-bm| bm v|-|;-vvb]ml;m|ĺ);=buv|v;lѴ|b;;m|lo7;Ѵv|o;v|bl-|;vub-Ѵ -m77;|;1|bomr-u-l;|;uvĸv;1om7ķ;v;|_;(b|;u0b-Ѵ]oub|_l|o-vŊ vb]m|_;m1;u|-bmo0v;u;7bm7bb7-Ѵv|o|_;lov|Ѵbh;Ѵv|-|;Ő!o-mķ -bѴѴ-u7ķ࣐7omķşu-7;ѴķƑƏƏƖĸ,11_bmbķ-1 om-Ѵ7ķş-m]uo1hķ ƑƏƏƖőķ-m7Ѵ-v|Ѵķ;;v|bl-|;ru;-Ѵ;m1;b--oub|ŋ$_olrvomŊѴbh; estimator combined with a bootstrapping procedure to produce stanŊ 7-u7;uuou-m71om=b7;m1;bm|;u-ѴvŐ -bvomşbmhѴ;ķƐƖƖƕőĺ
); -vv;vv |_; blrou|-m1; o= bm1ourou-|bm] 7;|;1|-0bѴb| -m7 m1;u|-bm| bm v|-|; -vvb]ml;m| 0 1olr-ubm] |_; r;u=oul-m1; o= lo7;ѴŊ0-v;7-m7m-b;ru;-Ѵ;m1;m7;u7b==;u;m|v1;m-ubovĺ$_;-1Ŋ 1u-1o=!r-u-l;|;uvĽ;v|bl-|ouv7;r;m7vom|_;u;1-r|u;u-|; -m7om|_;ml0;uo=1-r|u;o11-vbomvŐ|bv;|-ѴĺķƐƖƕѶőĺm1u;-vbm] |_;7;|;1|-0bѴb|-m7ņou|_;ml0;uo=o11-vbomvu;tbu;v7b==;u;m| sampling strategies and generates different costs in terms of financial -m7_l-mu;vou1;vŐb;u;|-ѴĺķƑƏƐƕőĺ$_;u;=ou;ķ;-Ѵvo;rѴou; _o7b==;u;m|v-lrѴbm]v|u-|;]b;vl--==;1||_;lo7;Ѵr;u=oul-m1;ĺ
Despite the increasing attention that researchers are devoting to _0ub7b-|bom1-v;vŐ"1_;mhķu;7;ķş"|u;b|ķƑƏƏѶĸ$o7;v1o;|-Ѵĺķ ƑƏƐѵőķ|_;u;_-;0;;momѴ =; -||;lr|v|o;v|bl-|;ru;-Ѵ;m1; o=_0ub7vbmbѴ7rorѴ-|bomvŐ(-bm|oķ;f-ķ ;uu-m7ķşo7bm_oķ ƑƏƐƔőĺ);bѴѴv|u-|;oul;|_o7b|_-1-v;v|70;v|bl-|bm]|_; ru;-Ѵ;m1;o=oѴ=ŐCanis lupusőƵ7o]ŐCanis lupus familiariső_0ub7v bm-oѴ=rorѴ-|bombmmou|_;um|-Ѵĺ$_bvbv-1-v;o=-m|_uoro];mb1 _0ub7b-|bomŐbĺ;ĺķ|_;bm|;u0u;;7bm]o=bm7bb7-Ѵv=uol];m;|b1-ѴѴ 7bv|bm1| rorѴ-|bomv 7; |o _l-m -1|bomĸ ѴѴ;m7ou= ;|-Ѵĺķ ƑƏƏƐő -m7bv1omvb7;u;7-l-fou|_u;-||ooѴ=];molb1bm|;]ub|Őob|-mbķ ƑƏƏƏőĺ $_;u;=ou;ķ -11u-|;Ѵ ;v|bl-|bm] |_; ru;-Ѵ;m1; o= _0ub7v bm oѴ= rorѴ-|bomv bv - ruboub| |o ;Ѵ-0ou-|; 1omv;u-|bom v|u-|;Ŋ ]b;vŐbm7ub1hvom;|-ѴĺķƑƏƐƕőĺ);v_o|_-|bm|_bv1-v;vbm]m-b; ru;-Ѵ;m1;-v-ruom7;u;v|bl-|;v|_;ru;-Ѵ;m1;o=_0ub7vĺ ƑՊ|Պ$ " ƑĺƐՊ|Պb77;m-uholo7;Ѵ );-vvl;7|_-|-mbl-Ѵv-u;bm7bb7-ѴѴu;1o]mb;7-|7bv1u;|;;mŊ 1om|;uo11-vbomvķ|_;u;=ou;o0|-bmbm]-m;m1om|;u_bv|ou=ou;-1_
ƕƓѵՊ
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SANTOSTASI ETAL.v|-|;vĹ-Ѵb;-m7r-u;m|-ѴŐőķ-Ѵb;-m7_0ub7Őőķou7;-7Ő őĺ); m7;uѴbm;|_-|_;u;-=|;u|_;|;ulľ_0ub7Ŀu;=;uv|o-ѴѴ1-|;]oub;vo= -7lb|u;-m7mo|omѴ|o=buv|Ŋ];m;u-|bom_0ub7vĺ&romb|v=buv|;mŊ 1om|;uķ-mbm7bb7-Ѵ_-v-ruo0-0bѴb|πp to be a parental and the
1olrѴ;l;m|-uruo0-0bѴb|πhƷƐƴπp|o0;-_0ub7ĺ$_;bmb|b-Ѵv|-|;
ruo0-0bѴb|b;v7;v1ub0;|_;ruo0-0bѴb||_-|-mbm7bb7-Ѵbvbmom;ou -mo|_;uv|-|;_;m=buv|;m1om|;u;7ĺ$_;mķ|_;v|-|;v1_-m];o;u |bl;-11ou7bm]|o-=buv|Ŋou7;u-uhoruo1;vvķb|_|_;v|-|;ruoŊ 1;vv 0;bm] ]o;um;7 0 -rr-u;m| vub-Ѵ ruo0-0bѴb|b;v φp and φh.
ou;vr;1b=b1-ѴѴķ|_;v|-|;ruo1;vvķ_b1_vll-ub;v|_;m7;uѴŊ bm]0boѴo]b1-Ѵruo1;vvķbvu;ru;v;m|;70-|u-mvb|bomruo0-0bѴb|l-Ŋ |ubb|_v|-|;v-||bl;tbmuovŐľ-u;m|-ѴķĿľ0ub7ķĿľ ;-7Ŀő-m7
t + Ɛbm1oѴlmvŐľ-u;m|-ѴķĿľ0ub7ķĿľ ;-7ĿőĹ
where parameter φp Őu;vrĺ φhő bv |_; ruo0-0bѴb| |_-| -m bm7bb7-Ѵ
-Ѵb;-m7bmv|-|;ľ-u;m|-ѴĿŐu;vrĺľ0ub7Ŀő-||bl;t is still alive in |_;v|7-u;--m7bmv|-|;ľ-u;m|-ѴĿŐu;vrĺľ0ub7Ŀő-||bl;t + 1 -m7 1ouu;vrom7v |o |_; -rr-u;m| vub-Ѵ ruo0-0bѴb| o= r-u;m|-Ѵ Őu;vrĺľ0ub7Ŀőbm7bb7-Ѵvĺ
$_; v;1om7 |bl; v;ub;v Őou ;;m| ruo1;vvő bv ];m;u-|;7 =uol the states at each occasion and describes the observation proŊ cess. Individuals are detected at time tb|_ruo0-0bѴb|o=7;|;1Ŋ tion pp for parental and ph=ou_0ub7bm7bb7-Ѵvĺ&rom7;|;1|bomķ -m-||;lr|bvl-7;o=-vvb]mbm]|_;bm7bb7-Ѵv|o-_0ub7b-|bom state based on genetic and/or morphologic diagnostic features -m7 |_;u; bv - ruo0-0bѴb| δ that an individual is assigned to the v|-|; ľ-u;m|-ѴĿ ou ľ0ub7Ŀĺ = |_; 7b-]mov|b1 1Ѵ;v -u; mo| v=Ŋ =b1b;m||o-v1;u|-bm|_;_0ub7b-|bomv|-|;ķ|_;bm7bb7-Ѵbv1Ѵ-vŊ vb=b;7-vm1;u|-bmb|_|_;1olrѴ;l;m|-uruo0-0bѴb|Ɛƴδ. The o0v;u-|bomruo1;vvbvvll-ub;70-l-|ubb|_v|-|;vbmuov Őľ-u;m|-ѴķĿ ľ0ub7ķĿ ľ ;-7Ŀő -m7 ;;m|v bm 1oѴlmv ŐƏƷľo| 7;|;1|;7ķĿ ƐƷľ ;|;1|;7 -v r-u;m|-ѴķĿ ƑƷľ ;|;1|;7 -v _0ub7ķĿ ƒƷľ ;|;1|;7-vm1;u|-bmĿőĹ
7;-7ĺtb-Ѵ;m|Ѵķ|_;;;m|ruo1;vv1-m0;7;1olrov;7-v|_; ruo71|o=-7;|;1|boml-|ub0-m-vvb]ml;m|l-|ub_b1_;Ŋ ru;vv;v|_;ruo0-0bѴb||_-|-mbm7bb7-Ѵbv-vvb]m;7|o-v|-|; given that it has been detected:
_;m -m -mbl-Ѵ bv =buv| ;m1om|;u;7ķ |_; 1-r|u; ruo1;vv bv mo| modeled because an animal must be encountered at least once to ;m|;u|_;7-|-v;|ķ0||_;v|-|;-v1;u|-bml;m|u;l-bmv-Ѵb7ĺ
$obѴѴv|u-|;|_;1-Ѵ1Ѵ-|bomo=-m;m1om|;u_bv|ouķѴ;|v1omŊ vb7;u |_; 1-v; o= - ƒŊ;-u ! ;r;ubl;m|ĺ ou bmv|-m1;ķ |_; ;mŊ 1om|;u _bv|ou ľƒƏƒĿ 7;mo|;v -m bm7bb7-Ѵ ;m1om|;u;7 -| |_; first and third occasions but not at the second occasion. The state o=|_bvbm7bb7-Ѵbvm;;u-vvb]m;7ĺvvlbm]r-u-l;|;uv-u;1omŊ v|-m|ķ;_-;
m |_; ub]_| vb7; o= |_; ;t-|bomķ |_; =buv| ;Ѵ;l;m| o= |_; vlbv|_;ruo0-0bѴb|o=|_;o0v;u;7_bv|oub=|_;m7;uѴbm] v|-|;bvľ0ub7Ŀķ_bѴ;|_;v;1om7;Ѵ;l;m|bv|_;ruo0-0bѴb|o= |_;o0v;u;7_bv|ou]b;m|_-||_;m7;uѴbm]v|-|;bvľ-u;m|-ѴĿĺ The likelihood of the entire dataset is obtained as the product of the probabilities of all individual encounter histories assumŊ bm] bm7;r;m7;m1;ĺ m |_bv r-r;uķ ;v|bl-|;v o= bmb|b-Ѵ v|-|;v Őπp
and πhőķ-rr-u;m|vub-ѴŐφp and φhőķ7;|;1|bomŐpp and phőķ-m7 -vvb]ml;m|ruo0-0bѴb|b;vŐδp and δhő-u;o0|-bm;70l-blbbm]
|_;Ѵbh;Ѵb_oo7=m1|bomĺ b==;u;m|lo7;Ѵv1-m0;0bѴ|0-ѴѴobm] |_;r-u-l;|;uv|o-u-11ou7bm]|oķ=ou;-lrѴ;ķv|-|;ķ|bl;ķou ]uor o= bm7bb7-Ѵv 1Ѵ-vvb=b;7 0-v;7 om 7bv1u;|; -ub-0Ѵ;v Ő;ĺ]ĺķ -];1Ѵ-vvouv;őĺ
ƑĺƑՊ|Պ0m7-m1;-m7ru;-Ѵ;m1;;v|bl-|bom
-b;ru;-Ѵ;m1;ŐPnaiveő-|-]b;mo11-vbombv1-Ѵ1Ѵ-|;7-v|_;ruoŊ
rou|bomo=o0v;u;7_0ub7vbm|_;v-lrѴ;Ĺ ⎛ ⎜ ⎜ ⎜ ⎝ P H D P 𝜑p 0 1− 𝜑p H 0 𝜑h 1− 𝜑h D 0 0 1 ⎞ ⎟ ⎟ ⎟ ⎠ ⎛ ⎜ ⎜ 0 1 2 3 P 1− pp pp𝛿 p 0 pp(1−𝛿p) H 1− ph 0 ph𝛿h ph(1−𝛿h) ⎞ ⎟ ⎟ ⎛ ⎜ ⎜ ⎜ ⎝ 0 1 2 P 1 − pp pp 0 H 1− ph 0 ph D 1 0 0 ⎞ ⎟ ⎟ ⎟ ⎠ ⎛ ⎜ ⎜ ⎜ ⎝ 0 1 2 3 0 1 0 0 0 1 0 𝛿p 0 1−𝛿p 2 0 0 𝛿 h 1−𝛿h ⎞ ⎟ ⎟ ⎟ ⎠ Pr(303) = 𝜋h(1 − 𝛿h) 𝜑h(1 − ph) 𝜑hph(1 − 𝛿h ) +𝜋p(1 − 𝛿p) 𝜑p(1 − pp) 𝜑ppp(1 − 𝛿p)
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ՊƕƓƕSANTOSTASI ETAL.
where nhbv|_;ml0;uo=o0v;u;7_0ub7vķ-m7np is the number o=o0v;u;7r-u;m|-Ѵbm7bb7-Ѵvķ ̂phbv|_;u;1-r|u;ruo0-0bѴb|o=
_0ub7vķ-m7 ̂ppbv|_;u;1-r|u;ruo0-0bѴb|o=r-u;m|-Ѵbm7bb7-Ѵvĺ
o7;ѴŊ0-v;7ru;-Ѵ;m1;bv|_;m;v|bl-|;7-vĹ
$_; l-bm 7b==b1Ѵ| bv |_;u;=ou; bm 7;|;ulbmbm] |_; ml0;u o= o0v;u;7 r-u;m|-Ѵ bm7bb7-Ѵv -m7 _0ub7vķ 0;1-v; |_; m1;u|-bm bm7bb7-Ѵv_-;|o0;-vvb]m;7|oom;o=|_;|ov|-|;vŐľ0ub7Ŀ ouľ-u;m|-ѴĿőĺ$o7ovoķ;v;|_;(b|;u0b-Ѵ]oub|_lŐ,11_bmb;|-Ѵĺķ ƑƏƏƖő _b1_ķ ]b;m -m o0v;u-|bom v;t;m1; Ő_;u;ķ |_; ;m1omŊ |;u_bv|oub;vő-m7|_;r-u-l;|;uv;v|bl-|;70|_;_b77;m-uho lo7;Ѵķ=bm7v|_;lov|ruo0-0Ѵ;m7;uѴbm]v;t;m1;o=v|-|;v|_-| _-v ];m;u-|;7 |_; o0v;u;7 7-|- Ő!o-m ;|-Ѵĺķ ƑƏƏƖőĺ m1; |_; m1;u|-bm o0v;u-|bomv -u; -vvb]m;7 |o |_; lov| Ѵbh;Ѵ v|-|;ķ |_; ml0;uo=o0v;u;7_0ub7-m7r-u;m|-Ѵbm7bb7-Ѵv1-m0;u;1omŊ v|u1|;7-m7|_;=oulѴ-1-m0;v;7|o;v|bl-|;ru;-Ѵ;m1;ĺ); o0|-bm 1om=b7;m1; bm|;u-Ѵv =ou |_; _0ub7vĽ ru;-Ѵ;m1; 0 vbm] - momr-u-l;|ub10oo|v|u-rruo1;7u;Ő -bvomşbmhѴ;ķƐƖƖƕőĺ ƑĺƒՊ|Պ-Ѵ-|bomo=lo7;Ѵr;u=oul-m1;-m7 v-lrѴbm]v|u-|;] $o|;v||_;lo7;Ѵr;u=oul-m1;ķ;];m;u-|;7;m1om|;u_bv|oŊ ub;vb|_hmomru;-Ѵ;m1;lblb1hbm]ou1-v;v|7omoѴ;v -m77o]vbm|_;ou|_;umr;mmbm;vŐv;;m;|v;1|bomő-m71olŊ r-u;7lo7;ѴŊ0-v;7ru;-Ѵ;m1;-m7m-b;ru;-Ѵ;m1;ĺ&vbm]|_; !Ő!ou;$;-lķƑƏƐƕőr-1h-];Őbll;Ѵl-mmķƑƏƐƏőķ; simulated a cohort of 100 individuals that we split into 2 states ľ0ub7Ŀ-m7ľ-u;m|-ѴĿĺ ou-ѴѴ|_;v1;m-ubovķ;v;||_;bmb|b-Ѵ proportion of wolves πpƷƏĺƕ -m7 bmb|b-Ѵ ruorou|bom o= _0ub7v πhƷƐƴπpƷƏĺƒ -v bm ou 1-v; v|7 v-lrѴ; Őv;; m;| v;1|bomőĺ &vbm]-Ѵ;v;v|bl-|;70-mb]Ѵb-;|-ѴĺŐƑƏƐƑő=ou|_;v-l;oѴ= rorѴ-|bomķ ; 1omvb7;u;7 v|-|;Ŋ7;r;m7;m| vub-Ѵ Ő1omv|-m| o;u|bl;őb|_r-u;m|-Ѵvub-ѴŐφpƷƏĺѶő_b]_;u|_-m_0ub7vuŊ
b-ѴŐφhƷƏĺƕőĺ);|_;m1omvb7;u;7|_u;;_ro|_;|b1-Ѵv1;m-ubov
=ou7;|;1|-0bѴb|-m7-vvb]ml;m|ruo0-0bѴb|ĹŐv;;"rrou|bm]bmŊ formation Table S1 for a complete list of parameters for the three v1;m-ubovőŐƐőv|-|;Ŋ7;r;m7;m|7;|;1|-0bѴb|Őpp > phő-m7_oloŊ
];m;ov -vvb]ml;m| ruo0-0bѴb|ķ ŐƑő _olo];m;ov 7;|;1|-0bѴŊ b|-m7v|-|;Ŋ7;r;m7;m|-vvb]ml;m|ruo0-0bѴb|Őδp > δhő-m7Őƒő
_olo];m;ov 7;|;1|-0bѴb| -m7 -vvb]ml;m| ruo0-0bѴb|ĺ )b|_bm |_;v; |_u;; l-bm v1;m-ubovķ ; ;-Ѵ-|;7 |_; ;==;1| o= Ѵo;u -m7 _b]_;u v-lrѴbm] bm|;mvb|b;v 0 1olr-ubm] v-lrѴbm] v|u-|;Ŋ ]b;vb|_Ѵo-m7_b]_7;|;1|-0bѴb|-m7b|_Ɣ-m7ƐƏ1-r|u; o11-vbomvĺ ); vblѴ-|;7 ƐƏƏ 7-|-v;|v =ou ;-1_ 1ol0bm-|bom o= r-u-l;|;uvb|_bm|_;|_u;;l-bmv1;m-ubovĺ);=b||;71omv|-m| -m7v|-|;Ŋ7;r;m7;m|lo7;Ѵv|o|_;vblѴ-|;77-|-ķ-m7;1-ѴŊ 1Ѵ-|;7|_;u;Ѵ-|b;0b-v-m7|_;uoo|l;-mvt-u;7;uuouŐ!"ő =ou |_; lo7;ѴŊ0-v;7 -m7 |_; m-b; ru;-Ѵ;m1; ;v|bl-|ouvĺ );
-Ѵvo1-Ѵ1Ѵ-|;7|_;1om=b7;m1;bm|;u-Ѵ1o;u-];=ou|_;lo7;ѴŊ based estimator of prevalence.
ƑĺƓՊ|Պ-v;v|7
); 1oѴѴ;1|;7 =u;v_ oѴ= v1-|v bm |_; rr;mmbmo $ov1oŊ;lbѴb-mo -|bom-Ѵ -uh =uol ]v| ƑƏƐѵ |o - ƑƏƐƕĺ ); ;|u-1|;7ķ -lrѴb=b;7-m7v;t;m1;7 =uol|_;v1-|v=oѴѴobm]|_;ruoŊ 1;7u;v 7;v1ub0;7 bm -mb]Ѵb-ķ -00ubķ -Ѵ-;umbķ bѴ-m;vbķ -m7 !-m7b ŐƑƏƐƓőĺ ); b7;m|b=b;7 oѴ;vķ 7o]v -m7 r|-|b; _0ub7v 0-v;7om|_;-m-Ѵvbvo=loѴ;1Ѵ-ul-uh;uvѴbv|;7bm!-m7b;|-Ѵĺ ŐƑƏƐƓő -m7 vbm] -;vb-m ];m;|b1 1Ѵv|;ubm] ruo1;7u;v blrѴ;Ŋ l;m|;7 bm "$!&$&! ƑĺƒĺƓ Ő -Ѵv_ķ "|;r_;mvķ ş ub|1_-u7ķ ƑƏƏƒĸub|1_-u7ķ"|;r_;mvķş omm;ѴѴķƑƏƏƏőĺ);7bv|bm]bv_;7 oѴ;vķ _0ub7vķ -m7 m1;u|-bm bm7bb7-Ѵv 0-v;7 om |_;bu l;lŊ 0;uv_brruorou|bomv|o|_;oѴ=1Ѵv|;uŐqwolfő-m7ƖƏѷ-;vb-m
1u;7b0Ѵ;bm|;u-ѴvŐőĺ);v;||_;|_u;v_oѴ7v=ou|_;|_u;;1-|Ŋ ;]oub;v 0-v;7 om |_; ];m;|b1 1Ѵv|;ubm] -m-Ѵv;v r;u=oul;7 om vblѴ-|;7];mo|r;v0-1_;1o;|-ѴĺŐƑƏƐƕőķv;; b]ĺ"Ɛbm|_; "rrѴ;l;m|-u-|;ub-Ѵvo=-1_;1o;|-ѴĺŐƑƏƐƕőĺ);1omvb7;u;7 as pure wolves those individuals whose qwolf was included in the range of qwolf-Ѵ;vo=vblѴ-|;7ru;oѴ;v];mo|r;v-m77b7 mo| o;uѴ-r b|_ |_-| o= vblѴ-|;7 0-1h1uovv;v Ő_0ub7Ƶr-u;mŊ |-Ѵőĺ);1Ѵ-vvb=b;7-vm1;u|-bm|_ov;bm7bb7-Ѵv_ov;qwolf was
included in the range in which the qwolf values of simulated pure oѴ;v -m7 0-1h1uovv;v |o oѴ;v Ő=buv| -m7 v;1om7 ];m;u-|bomő o;uѴ-rr;7ĺ bm-ѴѴķ ; 1omvb7;u;7 -v _0ub7v |_ov; bm7bb7-Ѵv whose qwolf overlapped with the range of qwolf values of simulated 0-1h1uovv;vŐ=buv|-m7v;1om7];m;u-|bomő-m7ņou_0ub7vŐ=buv|-m7 v;1om7];m;u-|bomőĺ);-77b|bom-ѴѴ1omvb7;u;7-v_0ub7v|_ov; bm7bb7-Ѵv_b1_ru;v;m|;7-+_-rѴo|r;o=1-mbm;oub]bmou|_; 7;Ѵ;|bom -| |_; ŊѴo1v Ő-mb]Ѵb- ;|-Ѵĺķ ƑƏƐƒĸ !-m7b ;|-Ѵĺķ ƑƏƐƓő regardless of their qwolf values.
$_;!7-|-;u;rooѴ;7bmƑŊlom|_1-r|u;o11-vbomvķb|_ - |o|-Ѵ o= =b; 1-r|u; o11-vbomvĺ $_bu|Ŋmbm; bm7bb7-Ѵv ;u; v-lrѴ;7ŐƐƖoѴ;vķƐƑ_0ub7vķѶm1;u|-bmv0-v;7om|_;buqwolf
-Ѵ;őĺ ); -rrѴb;7 |_; lѴ|b;;m| ! lo7;Ѵ 7;v1ub0;7 -0o; |o |;v| =ou 7b==;u;m1;v bm 7;|;1|-0bѴb| -m7 -vvb]ml;m| ruo0-0bѴb| 0;|;;m _0ub7 -m7 r-u;m|-Ѵ bm7bb7-Ѵv -m7 |o ;v|bl-|; ru;-Ŋ Ѵ;m1; o= oѴ=Ƶ7o] _0ub7v bm |_; rorѴ-|bomĺ "bm1; |_; _0ub7Ŋ b-|bom -vv;vvl;m| bv r;u=oul;7 omѴ om1; =ou ;-1_ ];mo|r;ķ ; 1omv|u-bm;7 |_; -vvb]ml;m| ruo0-0bѴb| |o 0; ;v|bl-|;7 omѴ rom =buv| 1-r|u; Őv;; |_; lo7;Ѵv 7;|-bѴv bm |_; "rrou|bm] bmŊ =oul-|bomőĺ);=b||;7lo7;Ѵvb|_v|-|;Ŋ7;r;m7;m|-m71omv|-m| parameters and a combination of the two. The models were fitted bm |_; Ŋ"&! vo=|-u; Ő_ot;|ķ !o-mķ ş u-7;Ѵķ ƑƏƏƖő -m7 |_;(b|;u0b-Ѵ]oub|_l-vblrѴ;l;m|;7vbm]|_;!Ő!ou;$;-lķ ƑƏƐƕő r-1h-]; Őbll;Ѵl-mmķ ƑƏƐƏőĺ ); v;7 |_; h-bh; m=oul-|bomub|;ubomŐő=oulo7;Ѵv;Ѵ;1|bomķ1omvb7;ubm]lo7Ŋ els within Δ1ƽƑ-v|_;lov|vrrou|;7-m7v;7lo7;Ѵ-;uŊ -]bm]|o-11om|=oum1;u|-bm|bmlo7;Ѵv;Ѵ;1|bomŐum_-lş m7;uvomķƑƏƏƑőĺ
Pmodel=
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ՊՊՍ SANTOSTASI ETAL. ƒՊ|Պ!"&$" ƒĺƐՊ|Պ-Ѵ-|bomo=lo7;Ѵr;u=oul-m1; -b;ru;-Ѵ;m1;_-7_b]_;u!"-m7r;u1;m|u;Ѵ-|b;0b-v|_-m lo7;ѴŊ0-v;7ru;-Ѵ;m1;bmv1;m-uboƐŐv|-|;Ŋ7;r;m7;m|7;|;1|-0bѴŊ b|-m7_olo];m;ov-vvb]ml;m|ruo0-0bѴb|ĸ b]u;Ɛķ$-0Ѵ;vƐķƑőĺ $_; v-l; o11uu;7 bm v1;m-ubo Ƒ Ő_olo];m;ov 7;|;1|-0bѴb| -m7 v|-|;Ŋ7;r;m7;m| -vvb]ml;m| ruo0-0bѴb|ĸ "rrou|bm] bm=oul-|bom b]u; "Ɛ -m7 $-0Ѵ;v "Ƒķ "ƒőĺ -b; -m7 lo7;ѴŊ0-v;7 ru;-Ѵ;m1; _-7vblbѴ-u!"-m7u;Ѵ-|b;0b-vomѴbmv1;m-uboƒŐ_olo];m;ov 7;|;1|-0bѴb| -m7 -vvb]ml;m| ruo0-0bѴb|ĸ "rrou|bm] bm=oul-|bom b]u;"Ɛ-m7$-0Ѵ;v"Ɠķ"Ɣőĺ $_;0b-v-vvo1b-|;7b|_lo7;ѴŊ0-v;7ru;-Ѵ;m1;|;m7;7|oƏbm & ! Ɛ Պ "1;m-uboƐo=vblѴ-|bomŐv|-|;Ŋ7;r;m7;m|7;|;1|-0bѴb|-m7_olo];m;ov-vvb]ml;m|ruo0-0bѴb|őĺ"-lrѴbm]v|u-|;]b;vb|_ ƔŐrr;ur-m;Ѵvő;uvvƐƏŐѴo;ur-m;Ѵvő1-r|u;o11-vbomv-m7ѴoŐѴ;=|Ŋ1oѴlmr-m;Ѵvő;uvv_b]_Őub]_|Ŋ1oѴlmr-m;Ѵő7;|;1|-0bѴb|ĺ$u; ru;-Ѵ;m1;bvu;ru;v;m|;7-v-7-v_;7Ѵbm;_bѴ;|_;ƐƏƏ-Ѵ;vo=m-b;-m7lo7;ѴŊ0-v;7ru;-Ѵ;m1;-u;7bvrѴ-;7bm|_;_b|;-m7]u- 0orѴo|vķu;vr;1|b;Ѵ $ Ɛ Պ "1;m-uboƐo=vblѴ-|bomŐv|-|;Ŋ7;r;m7;m| 7;|;1|-0bѴb|-m7_olo];m;ov-vvb]ml;m|ruo0-0bѴb|ő 11ĺƐ 11ĺƑ 11ĺƒ 11ĺƓ 11ĺƔ !oo|l;-mvt-u;7;uuou o7;|;1|-0bѴb| -b; 0.07 0.14 0.23 0.23 0.30 o7;ѴŊ0-v;7 0.30 0.15 ƏĺƏѵ 0.07 0.02 b]_7;|;1|-0bѴb| -b; ƏĺƑѵ Əĺƒѵ 0.48 0.41 0.48 o7;ѴŊ0-v;7 0.04 0.02 0.00 0.01 0.00 ;u1;m|u;Ѵ-|b;0b-v|
ՊƕƓƖ SANTOSTASI ETAL. v_o;70|_;0orѴo|Ѵ-u];uu-m];vŐ b]u;vƑŋƓĸ"rrou|bm]bm=ouŊ l-|bom b]u;v"Ƒŋ"ƐƏőĺ om=b7;m1;bm|;u-Ѵ1o;u-];-v-Ѵ-vƾƏĺѶƖ=ou-ѴѴv1;m-ubov b|_Ɣv-lrѴbm]o11-vbomvŐ$-0Ѵ;ƒĸ"rrou|bm]bm=oul-|bom$-0Ѵ;v "ѵķ"ƕőĺ ouv1;m-ubovb|_ƐƏo11-vbomvŐ$-0Ѵ;Ɠĸ"rrou|bm]bm=ouŊ l-|bom$-0Ѵ;v"Ѷķ"Ɩő1o;u-];7;1u;-v;7-=|;u|_;ƕ|_ŋѶ|_o11-Ŋ ;m7o=|_;v|7Ő7;|o-Ѵo-rr-u;m|vub-Ѵő-==;1|v|_;-11u-1 o=|_;;v|bl-|;vŐ b]u;Ɛĸ"rrou|bm]bm=oul-|bom b]u;v"Ɛķ"Ƒőĺ ƒĺƑՊ|Պ-Ѵ-|bomo=v-lrѴbm]v|u-|;]b;v $_;r;u=oul-m1;o=lo7;ѴŊ0-v;7ru;-Ѵ;m1;blruo;7lou;-| $ Ƒ Պ "1;m-uboƐo=vblѴ-|bomŐv|-|;Ŋ7;r;m7;m|7;|;1|-0bѴb|-m7_olo];m;ov-vvb]ml;m|ruo0-0bѴb|ő 11ĺƐ 11ĺƑ 11ĺƒ 11ĺƓ 11ĺƔ 11ĺѵ 11ĺƕ 11ĺѶ 11ĺƖ 11ĺƐƏ !oo|l;-mvt-u;7;uuou o7;|;1|-0bѴb| -b; 0.14 0.22 0.21 0.33 0.33 0.30 0.40 Əĺƒѵ ƏĺƑѵ 0.78 o7;ѴŊ0-v;7 0.1 0.04 0.05 0.01 0.01 0.00 0.00 0.00 0.02 0.02 b]_7;|;1|-0bѴb| -b; 0.23 0.51 0.37 0.45 0.49 0.50 0.39 Əĺƒѵ ƏĺƐѵ ƏĺƐѵ o7;ѴŊ0-v;7 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ;u1;m|u;Ѵ-|b;0b-v o7;|;1|-0bѴb| -b; ƴƏĺƏƓ ƴƏĺƏƔ ƴƏĺƏƔ ƴƏĺƏѵ ƴƏĺƏѵ ƴƏĺƏƔ ƴƏĺƏѵ ƴƏĺƏѵ ƴƏĺƏƔ ƴƏĺƏƒ o7;ѴŊ0-v;7 ƴƏĺƏƒ ƴƏĺƏƑ ƴƏĺƏƑ ƴƏĺƏƐ ƴƏĺƏƐ ƴƏĺƏƏ ƴƏĺƏƏ ƴƏĺƏƐ ƴƏĺƏƐ ƴƏĺƏƐ b]_7;|;1|-0bѴb| -b; ƴƏĺƏƔ ƴƏĺƏƕ ƴƏĺƏѵ ƴƏĺƏƕ ƴƏĺƏƕ ƴƏĺƏƕ ƴƏĺƏѵ ƴƏĺƏѵ ƴƏĺƏƓ ƴƏĺƏƓ o7;ѴŊ0-v;7 0.01 0.00 0.01 0.00 0.01 0.01 0.00 0.01 0.01 0.00 Noteĺ!oo|l;-mvt-u;7;uuou-m7u;Ѵ-|b;0b-vo=m-b;-m7lo7;ѴŊ0-v;7ru;-Ѵ;m1;=ouv-lrѴbm]v|u-|;]b;vb|_ƐƏ1-r|u;o11-vbomvŐ11őĺ& ! Ƒ Պ Scenario 1 of simulation Őv|-|;Ŋ7;r;m7;m|7;|;1|-0bѴb|-m7 _olo];m;ov-vvb]ml;m|ruo0-0bѴb|őĺ orѴo|vo=ƐƏƏvblѴ-|;7vub-Ѵ ;v|bl-|;v=our-u;m|-ѴvŐѴ;=||or-m;Ѵvő -m7_0ub7vŐub]_||or-m;Ѵvő=ou;-1_ v-lrѴbm]v|u-|;]ĺ"-lrѴbm]v|u-|;]b;v b|_Ѵo7;|;1|-0bѴb|-u;bm|_;|or uoķ-m7v-lrѴbm]v|u-|;]b;vb|__b]_ 7;|;1|-0bѴb|-u;bm|_;0o||oluoĺ Estimates obtained with sampling strategies with 5 and 10 capture occasions are compared in each panel
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SANTOSTASI ETAL.=uol Ѵo |o _b]_ĺ m 1om|u-v|ķ bm v-lrѴbm] v|u-|;]b;v b|_ Ѵo 7;|;1|-0bѴb|ķ |_; !" -m7 |_; u;Ѵ-|b; 0b-v o= lo7;ѴŊ0-v;7 ru;-Ѵ;m1; 7;1u;-v;7 Ѵ;vv u-rb7Ѵ =uol Ɣ |o ƐƏ 1-r|u; o11-Ŋ vbomvŐ b]u;Ɛķ$-0Ѵ;vƐķƑőĺ);o0v;u;7|_;v-l;r-||;um0o|_ bmv1;m-uboƑŐ"rrou|bm]bm=oul-|bom b]u;v"Ɛķ"Ƒķ$-0Ѵ;v"Ƒķ "ƒő-m7bmv1;m-uboƒķ-Ѵ|_o]_bm|_;Ѵ-||;u|_;0b-v-vvl-ѴѴu;Ŋ ]-u7Ѵ;vvo=|_;v-lrѴbm]v|u-|;]Ő"rrou|bm]bm=oul-|bom$-0Ѵ;v "Ɠķ"Ɣőĺ ƒĺƒՊ|Պ-v;v|7 $_;0;v|Ŋvrrou|;7lo7;Ѵ_-71omv|-m|r-u-l;|;uvŐ$-0Ѵ;Ɣőĺ o7;Ѵv b|_ v|-|;Ŋ7;r;m7;m| -rr-u;m| vub-Ѵķ 7;|;1|-0bѴb|ķ -m7 ruo0-0bѴb| o= -vvb]ml;m| ;u; -Ѵvo vrrou|;7 ŐΔ1ƺƑőĺ $_;lo7;Ѵvb|_v|-|;Ŋ7;r;m7;m|ruo0-0bѴb|o=-vvb]ml;m|;u; mo|b7;m|b=b-0Ѵ;7;|o|_;u;71;7v-lrѴ;vb;ķ-m7;7bv1-u7;7
& ! ƒ Պ Scenario 1 of simulation Őv|-|;Ŋ7;r;m7;m|7;|;1|-0bѴb|-m7 _olo];m;ov-vvb]ml;m|ruo0-0bѴb|őĺ orѴo|vo=ƐƏƏvblѴ-|;77;|;1|-0bѴb| ;v|bl-|;v=our-u;m|-ѴvŐѴ;=||or-m;Ѵvő -m7_0ub7vŐub]_||or-m;Ѵvő=ou;-1_ v-lrѴbm]v|u-|;]ĺ"-lrѴbm]v|u-|;]b;v b|_Ѵo7;|;1|-0bѴb|-u;bm|_;|or uoķ-m7v-lrѴbm]v|u-|;]b;vb|__b]_ 7;|;1|-0bѴb|-u;bm|_;0o||oluoĺ Estimates obtained with sampling strategies with 5 and 10 capture occasions are compared in each panel