Apparent survival estimation from continuous mark-recapture/resighting data

Novel passive detection approach reveals low breeding season survival and apparent lactation cost in a critically endangered cave bat

Capture-mark-recapture/resight (CMR) methods are used for survival-rate studies, yet are often limited by small sample sizes. Advances in passive integrated transponder (PIT) technology have enabled passive detection or ‘resight’ of marked individuals using large antennas with greater read-ranges than previously possible. We used passively-detected resight data and CMR models to study survival rates of the southern bent-winged bat Miniopterus orianae bassanii, a critically endangered, cave-dwelling bat. Over three years, we used PIT-tagging to monitor 2966 individuals at the species’ largest breeding aggregation, using daily detection data (> 1.6 million detections) to estimate seasonal survival probabilities, structured by age, sex and reproductive status, and parameterise population projection matrices. This has hitherto been impossible using traditional CMR methods due to disturbance risk and low recapture rates. Bats exhibited lowest apparent seasonal survival over summer and autumn, particularly for reproductive females in summer (when lactating) and juveniles in autumn (after weaning), and high survival in winter. Lowest survival rates coincided with severe drought in summer–autumn 2016, suggesting that dry conditions affect population viability. Under all likely demographic assumptions, population projection matrices suggested the population is in deterministic decline, requiring urgent action to reduce extinction risk. Passively-collected resight data can now be used in combination with CMR models to provide extensive, robust information for targeted wildlife population management.

Maximum approximate likelihood estimation of general continuous-time state-space models

Continuous-time state-space models (SSMs) are flexible tools for analysing irregularly sampled sequential observations that are driven by an underlying state process. Corresponding applications typically involve restrictive assumptions concerning linearity and Gaussianity to facilitate inference on the model parameters via the Kalman filter. In this contribution, we provide a general continuous-time SSM framework, allowing both the observation and the state process to be non-linear and non-Gaussian. Statistical inference is carried out by maximum approximate likelihood estimation, where multiple numerical integration within the likelihood evaluation is performed via a fine discretization of the state process. The corresponding reframing of the SSM as a continuous-time hidden Markov model, with structured state transitions, enables us to apply the associated efficient algorithms for parameter estimation and state decoding. We illustrate the modelling approach in a case study using data from a longitudinal study on delinquent behaviour of adolescents in Germany, revealing temporal persistence in the deviation of an individual's delinquency level from the population mean.

Ongoing declines of woodland birds: Are restoration plantings making a difference?

Woodland birds are a species assemblage of conservation concern, and their persistence in fragmented agricultural landscapes is dependent on both the preservation of existing woodland remnants and the implementation of restoration plantings. However, little is known about the habitat-use and persistence of birds in fragmented agricultural landscapes. We present a detailed, population-oriented study of woodland birds in temperate eucalypt woodland restoration plantings and remnant woodland patches in the South-west Slopes bioregion of New South Wales, Australia. First, we undertook a 3-yr mark-recapture project to assess annual survival and site fidelity in restoration plantings and woodland remnants. We supplemented our recapture efforts with resightings of color-banded individuals. Second, we tracked individual birds of two species, Superb Fairywren (Malurus cyaneus) and Willie Wagtail (Rhipidura leucophrys), and documented snapshots of their home ranges and movement patterns during the breeding season. Annual survival in the woodland bird assemblage was lower than expected (51%). Home ranges of the Superb Fairywren were positively correlated with patch size, and were constrained by patch edges in linear sites. Superb Fairywrens and Willie Wagtails were more likely to travel longer distances between substrates while foraging in linear sites. Willie Wagtails engaged in significant gap-crossing (up to 400 m) between adjacent habitat patches. Our findings indicate that (1) patch isolation and certain patch configurations place resident birds at an energetic disadvantage, and (2) in our study area, woodland bird populations are continuing to decline. We recommend landscape-scale habitat restoration programs aim to address ongoing population declines. Studies such as ours conducted over longer time periods would provide a deeper understanding of habitat use and population processes of woodland birds in fragmented agricultural landscapes.

The fishing and natural mortality of large, piscivorous Bull Trout and Rainbow Trout in Kootenay Lake, British Columbia (2008-2013)

Background

Estimates of fishing and natural mortality are important for understanding, and ultimately managing, commercial and recreational fisheries. High reward tags with fixed station acoustic telemetry provides a promising approach to monitoring mortality rates in large lake recreational fisheries. Kootenay Lake is a large lake which supports an important recreational fishery for large Bull Trout and Rainbow Trout.

Methods

Between 2008 and 2013, 88 large (≥500 mm) Bull Trout and 149 large (≥500 mm) Rainbow Trout were marked with an acoustic transmitter and/or high reward ($100) anchor tags in Kootenay Lake. The subsequent detections and angler recaptures were analysed using a Bayesian individual state-space Cormack–Jolly–Seber (CJS) survival model with indicator variable selection.

Results

The final CJS survival model estimated that the annual interval probability of being recaptured by an angler was 0.17 (95% CRI [0.11–0.23]) for Bull Trout and 0.14 (95% CRI [0.09–0.19]) for Rainbow Trout. The annual interval survival probability for Bull Trout was estimated to have declined from 0.91 (95% CRI [0.76–0.97]) in 2009 to just 0.46 (95% CRI [0.24–0.76]) in 2013. Rainbow Trout survival was most strongly affected by spawning. The annual interval survival probability was 0.77 (95% CRI [0.68–0.85]) for a non-spawning Rainbow Trout compared to 0.41 (95% CRI [0.30–0.53]) for a spawner. The probability of spawning increased with the fork length for both species and decreased over the course of the study for Rainbow Trout.

Discussion

Fishing mortality was relatively low and constant while natural mortality was relatively high and variable. The results indicate that angler effort is not the primary driver of short-term population fluctations in the Rainbow Trout abundance. Variation in the probability of Rainbow Trout spawning suggests that the spring escapement at the outflow of Trout Lake may be a less reliable index of abundance than previously assumed. Multi-species stock assessment models need to account for the fact that large Bull Trout are more abundant than large Rainbow Trout in Kootenay Lake.