A flexible framework for spatial capture-recapture with unknown identities.

Camera traps or acoustic recorders are often used to sample wildlife populations. When animals can be individually identified, these data can be used with spatial capture-recapture (SCR) methods to assess populations. However, obtaining animal identities is often labor-intensive and not always possible for all detected animals.

The global contribution of invasive vertebrate eradication as a key island restoration tool.

Islands are global hotspots for biodiversity and extinction, representing ~ 5% of Earth's land area alongside 40% of globally threatened vertebrates and 61% of global extinctions since the 1500s. Invasive species are the primary driver of native biodiversity loss on islands, though eradication of invasive species from islands has been effective at halting or reversing these trends. A global compendium of this conservation tool is essential for scaling best-practices and enabling innovations to maximize biodiversity outcomes.

Spatial correlation structures for detections of individuals in spatial capture-recapture models.

Spatial capture-recapture (SCR) models are commonly used to estimate animal density from surveys on which detectors passively detect animals without physical capture, for example, using camera traps, hair snares, or microphones. An individual is more likely to be recorded by detectors close to its activity center, the centroid of its movement throughout the survey. Existing models to account for this spatial heterogeneity in detection probabilities rely on an assumption of independence between detection records at different detectors conditional on the animals' activity centers, which are treated as latent variables.

A latent capture history model for digital aerial surveys.

We anticipate that unmanned aerial vehicles will become popular wildlife survey platforms. Because detecting animals from the air is imperfect, we develop a mark-recapture line transect method using two digital cameras, possibly mounted on one aircraft, which cover the same area with a short time delay between them. Animal movement between the passage of the cameras introduces uncertainty in individual identity, so individual capture histories are unobservable and are treated as latent variables.

Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground.

As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds.

Stationary distribution of the linkage disequilibrium coefficient r.

The linkage disequilibrium coefficient r is a measure of statistical dependence of the alleles possessed by an individual at different genetic loci. It is widely used in association studies to search for the locations of disease-causing genes on chromosomes. Most studies to date treat r as a fixed property of two loci in a finite population, and investigate the sampling distribution of estimators due to the statistical sampling of individuals from the population.

Cluster capture-recapture to account for identification uncertainty on aerial surveys of animal populations.

Capture-recapture methods for estimating wildlife population sizes almost always require their users to identify every detected animal. Many modern-day wildlife surveys detect animals without physical capture-visual detection by cameras is one such example. However, for every pair of detections, the surveyor faces a decision that is often fraught with uncertainty: are they linked to the same individual? An inability to resolve every such decision to a high degree of certainty prevents the use of standard capture-recapture methods, impeding the estimation of animal density.

Circadian and circatidal clocks control the mechanism of semilunar foraging behaviour.

How animals precisely time behaviour over the lunar cycle is a decades-old mystery. Experiments on diverse species show this behaviour to be endogenous and under clock control but the mechanism has remained elusive. We present new experimental and analytical techniques to test the hypotheses for the semilunar clock and show that the rhythm of foraging behaviour in the intertidal isopod, Scyphax ornatus, can be precisely shifted by manipulating the lengths of the light/dark and tidal cycles.

Empty forest or empty rivers? A century of commercial hunting in Amazonia.

The Amazon basin is the largest and most species-rich tropical forest and river system in the world, playing a pivotal role in global climate regulation and harboring hundreds of traditional and indigenous cultures. It is a matter of intense debate whether the ecosystem is threatened by hunting practices, whereby an "empty forest" loses critical ecological functions. Strikingly, no previous study has examined Amazonian ecosystem resilience through the perspective of the massive 20th century international trade in furs and skins.

Estimating the encounter rate variance in distance sampling.

The dominant source of variance in line transect sampling is usually the encounter rate variance. Systematic survey designs are often used to reduce the true variability among different realizations of the design, but estimating the variance is difficult and estimators typically approximate the variance by treating the design as a simple random sample of lines. We explore the properties of different encounter rate variance estimators under random and systematic designs.

Line transect sampling in small and large regions.

Melville and Welsh (2001, Biometrics 57, 1130-1137) consider an approach to line transect sampling using a separate calibration study to estimate the detection function g. They present a simulation study contrasting their results with poor results from a traditional estimator, labeled the "Buckland" estimator and referenced to Buckland et al. (1993, Distance Sampling: Estimating Abundance of Biological populations).