Spatial Capture-Recapture for Categorically Marked Populations with An Application to Genetic Capture-Recapture
Recently introduced unmarked spatial capture-recapture (SCR), spatial mark-resight (SMR), and 2-flank spatial partial identity models (SPIM) extend the domain of SCR to populations or observation systems that do not always allow for individual identity to be determined with certainty. For example, some species do not have natural marks that can reliably produce individual identities from photographs, and some methods of observation produce partial identity samples as is the case with remote cameras that sometimes produce single flank photographs. These models share the feature that they probabilistically resolve the uncertainty in individual identity using the spatial location where samples were collected. Spatial location is informative of individual identity in spatially structured populations with home range sizes smaller than the extent of the trapping array because a latent identity sample is more likely to have been produced by an individual living near the trap where it was recorded than an individual living further away from the trap. Further, the level of information about individual identity that a spatial location contains is determined by two key ecological concepts, population density and home range size. The number of individuals that could have produced a latent or partial identity sample increases as density and home range size increase because more individual home ranges will overlap any given trap. We show this uncertainty can be quantified using a metric describing the expected magnitude of uncertainty in individual identity for any given population density and home range size, the Identity Diversity Index (IDI). We then show that the performance of latent and partial identity SCR models varies as a function of this index and produces imprecise and biased estimates in many high IDI scenarios when data are sparse. We then extend the unmarked SCR model to incorporate partially identifying covariates which reduce the level of uncertainty in individual identity, increasing the reliability and precision of density estimates, and allowing reliable density estimation in scenarios with higher IDI values and with more sparse data. We illustrate the performance of this \"categorical SPIM\" via simulations and by applying it to a black bear data set using microsatellite loci as categorical covariates, where we reproduce the full data set estimates with only slightly less precision using fewer loci than necessary for confident individual identification. The categorical SPIM offers an alternative to using probability of identity criteria for classifying genotypes as unique, shifting the \"shadow effect\", where more than one individual in the population has the same genotype, from a source of bias to a source of uncertainty. We discuss the difficulties that real world data sets pose for latent identity SCR methods, most importantly, individual heterogeneity in detection function parameters, and argue that the addition of partial identity information reduces these concerns. We then discuss how the categorical SPIM can be applied to other wildlife sampling scenarios such as remote camera surveys, where natural or researcher-applied partial marks can be observed in photographs. Finally, we discuss how the categorical SPIM can be added to SMR, 2-flank SPIM, or other future latent identity SCR models.