Estimating abundance, temporary emigration and the pattern of density dependence in a cyclic snowshoe hare population in Yukon, Canada

Estimates of demographic parameters based on capture-mark-recapture (CMR) methods may be biased when some individuals in the population are temporarily unavailable for capture (temporary emigration). We estimated snowshoe hare abundance, apparent survival, and probability of temporary emigration in a population of snowshoe hares (Lepus americanus Erxleben 1777) in the Yukon using Pollock’s robust design CMR model, and population density using spatially-explicit CMR models. Survival rates strongly varied among cyclic phases, seasons, and across five population cycles. We found strong evidence that temporary emigration was Markovian (i.e., non-random), suggesting that it varied among individuals that were temporary emigrant in the previous sampling period and those that were present in the sampled area. The probability of temporary emigration for individuals that were in the study area during the previous sampling occasion (γ´´) varied among cycles. Probability that individuals that were temporarily absent from the sampled area would remain temporary emigrants (γ´) showed strongly seasonal pattern, low in winter and high during summers. Snowshoe hare population density ranged from 0.017 (0.015–0.05) hares/ha to 4.43 (3.90–5.00) hares/ha and large-scale cyclical fluctuation. Autocorrelation functions and autoregressive analyses revealed that our study population exhibited statistically significant cyclic fluctuations, with a periodicity of 9-10 years.

Out-of-sight or out-of-site? Forays and detection probabilities in single-season occupancy models

Occupancy models have become popular in wildlife survey analyses because they account for the frequent failure to detect individuals of targeted species. Those individuals sometimes move outside sampling sites, i.e. exhibit temporary emigration. In such cases, occupancy models may become difficult to interpret or even misleading either at the species or the individual level, because they confound presence at the site, availability for detection given presence, and actual detection by the observer. We quantified the probabilities of these three components with spruce grouse (Falcipennis canadensis) in southern Quebec, Canada. We conducted call-response surveys of 24 grouse monitored by radio-telemetry. We defined sites empirically as circular areas of 83 m radius centered on the observer, corresponding to the maximum detection distance obtained. Based on telemetry locations, grouse were present at the site during 42 % of the surveys. Six stationary grouse were present during surveys, but were never detected. Thus, only individuals that moved in the presence of the observer (89 %) were considered available for detection. Individuals available for detection were detected in 51 % of the cases. We simulated detection histories and built single-season occupancy models, based on the empirical relationship between detection probability and the distance measured between observers and grouse. When temporary emigration was ignored, site occupancy was ψ = 0.89, and the associated probability of detection was p = 0.23. When instances of temporary emigration were dropped, estimates were ψ = 0.88 and p = 0.41. Using only grouse available for detection, estimates were ψ = 0.87 and p = 0.42. Disentangling the components of detection probabilities had little impact on occupancy estimates, but showed a major effect of temporary emigration on estimated detection probabilities.

Abundance and demography of common bottlenose dolphins (Tursiops truncatus truncatus) in the Indian River Lagoon, Florida: A robust design capture-recapture analysis

Common bottlenose dolphins (Tursiops truncatus truncatus) inhabiting the Indian River Lagoon (IRL) estuarine system along the east coast of Florida are impacted by anthropogenic activities and have had multiple unexplained mortality events. Given this, managers need precise estimates of demographic and abundance parameters. Mark-recapture photo-identification boat-based surveys following a Robust Design were used to estimate abundance, adult survival, and temporary emigration for the IRL estuarine system stock of bottlenose dolphins. Models allowed for temporary emigration and included a parameter (time since first capture) to assess evidence for transient individuals. Surveys (n = 135) were conducted along predetermined contour and transect lines throughout the entire IRL (2016–2017). The best fitting model allowed survival to differ for residents and transients and to vary by primary period, detection to vary by secondary session, and did not include temporary emigration. Dolphin abundance was estimated from 981 (95% CI: 882–1,090) in winter to 1,078 (95% CI: 968–1,201) in summer with a mean of 1,032 (95% CI: 969–1,098). Model averaged seasonal survival rate for marked residents was 0.85–1.00. Capture probability was 0.20 to 0.42 during secondary sessions and the transient rate was estimated as 0.06 to 0.07. This study is the first Robust Design mark-recapture survey to estimate abundance for IRL dolphins and provides population estimates to improve future survey design, as well as an example of data simulation to validate and optimize sampling design. Transients likely included individuals with home ranges extending north of the IRL requiring further assessment of stock delineation. Results were similar to prior abundance estimates from line-transect aerial surveys suggesting population stability over the last decade. These results will enable managers to evaluate the impact of fisheries-related takes and provide baseline demographic parameters for the IRL dolphin population which contends with anthropogenic impacts and repeated mortality events.

Subterranean movement inferred by temporary emigration in Barton Springs salamanders (Eurycea sosorum)

Movement behavior is an important aspect of animal ecology but is challenging to study in species that are unobservable for some portion of their lives, such as those inhabiting subterranean environments. Using four years of robust-design capture-recapture data, we examined the probability of movement into subterranean habitat by a population of endangered Barton Springs salamanders (Eurycea sosorum), a species that inhabits both surface and subterranean groundwater habitats. We tested the effects of environmental variables and body size on survival and temporary emigration, using the latter as a measure of subterranean habitat use. Based on 2,046 observations of 1,578 individuals, we found that temporary emigration was higher for larger salamanders, 79% of which temporarily emigrated into subterranean habitat between primary sampling intervals, on average. Body size was a better predictor of temporary emigration and survival compared to environmental covariates, although coefficients from lower ranked models suggested turbidity and dissolved oxygen may influence salamander movement between the surface and subsurface. Surface population dynamics are partly driven by movement below ground and therefore surface abundance estimates represent a fraction of the superpopulation. As such, while surface habitat management remains an important conservation strategy for this species, periodic declines in apparent surface abundance do not necessarily indicate declines of the superpopulation associated with the spring habitat.

Use of genetic mark-recapture to estimate breeding site fidelity and philopatry in a threatened sea duck population, Alaska-breeding Steller’s eiders

The Steller’s eider Polysticta stelleri is a sea duck that breeds in Arctic tundra regions of Russia and Alaska (USA). The Alaska-breeding population is listed as ‘threatened’ under the US Endangered Species Act because of a perceived contraction of the breeding range in North America. Understanding demography of the listed population is critical for evaluating measures that can lead to increased abundance and thus, long-term viability. Specifically, estimates of return rates to breeding areas by adult females and natal areas by juvenile females are needed for planning effective recovery actions. We used a suite of polymorphic loci to genotype individuals and generated genetic profiles of nesting females and female offspring from nest materials collected between 1995 and 2016 in a ~170 km2 study area near Utqiagvik, Alaska. We analyzed capture histories of genetically identified individuals to estimate breeding site fidelity, temporary emigration, and philopatry. From a sample of 365 nests, we found that breeding site fidelity of adult females was high (0.91 ± 0.07 SE), and temporary emigration was also high (0.77 ± 0.06) and annually variable (range 0.34-0.97). From egg shell remains of 124 hatched females, we observed 9 recaptures as nesting adults, suggesting that philopatry was also high (range 0.6-1.0). Given the relatively high rates of adult female breeding site fidelity and female philopatry that we estimated, management actions that reduce mortality of adult females and increase annual productivity are likely to help maintain the population of a few hundred breeding Steller’s eiders on the Arctic Coastal Plain of Alaska.

Full-annual demography and seasonal cycles in a resident vertebrate

Wildlife demography is typically studied at a single point in time within a year when species, often during the reproductive season, are more active and therefore easier to find. However, this provides only a low-resolution glimpse into demographic temporal patterns over time and may hamper a more complete understanding of the population dynamics of a species over the full annual cycle. The full annual cycle is often influenced by environmental seasonality, which induces a cyclic behavior in many species. However, cycles have rarely been explicitly included in models for demographic parameters, and most information on full annual cycle demography is restricted to migratory species. Here we used a high-resolution capture-recapture study of a resident tropical lizard to assess the full intra-annual demography and within-year periodicity in survival, temporary emigration and recapture probabilities. We found important variation over the annual cycle and up to 92% of the total monthly variation explained by cycles. Fine-scale demographic studies and assessments on the importance of cycles within parameters may be a powerful way to achieve a better understanding of population persistence over time.

Robust design capture-recapture analysis of abundance and demographic parameters of Indian River Lagoon common bottlenose dolphins (Tursiops truncatus truncatus)

Accurate estimates of abundance are critical to species management and conservation. Common bottlenose dolphins (Tursiops truncatus truncatus) inhabiting the Indian River Lagoon (IRL) estuarine system along the east coast of Florida are impacted by anthropogenic activities and have had multiple unexplained mortality events, necessitating precise estimates of demographic and abundance parameters to implement management strategies. Mark-recapture methodology following a Robust Design survey was used to estimate abundance, adult survival, and temporary emigration for the IRL estuarine system stock of bottlenose dolphins. Models included a parameter (time since first capture) to assess evidence for transient individuals. Boat-based photo-identification surveys (n = 135) were conducted along predetermined contour and transect lines throughout the entire IRL (2016-2017). The best fitting model included the “transient” parameter to survival, allowed survival to vary by primary period, detection to vary by secondary session, and did not allow temporary emigration. Dolphin abundance ranged from 981 (95% CI: 882-1,090) in winter to 1,078 (95% CI: 968-1,201) in summer with a mean of 1,032 (95% CI: 969 -1,098). Model averaged seasonal survival rate for marked residents ranged from 0.85-1.00. Capture probability ranged from 0.20 to 0.42 during secondary sessions and transient rate from 0.06 to 0.07. This study represents the first Robust design mark-recapture survey effort to estimate abundance for IRL dolphins and provides parameter estimates to optimize sampling design of future studies. Transients included individuals with home ranges extending north of the IRL requiring further assessment of stock delineation. Results were remarkably similar to prior abundance estimates resulting from line-transect aerial surveys and were consistent with a stable population. Data will enable managers to evaluate the impact of fisheries-related takes as well as enable future comparisons of demographic parameters for a dolphin population that continues to sustain large scale mortality events and anthropogenic impacts.

Demography of the salt marsh harvest mouse (Reithrodontomys raviventris halicoetes) and associated rodents in tidal and managed wetlands

Suisun Marsh (Solano County, California) is the largest contiguous marsh remaining on the West Coast of the United States, and makes up approximately 10% of the wetlands remaining in the San Francisco Estuary. Suisun Marsh has been safeguarded from development through the operation of over 100 privately owned waterfowl hunting clubs, which manage for diked waterfowl habitat. However, this management—and the subsequent loss of tidal influence—has been considered harmful for some species, including the endangered salt marsh harvest mouse (SMHM; Reithrodontomys raviventris). To determine the value of tidal wetlands relative to those managed for waterfowl, we performed periodic surveys for rodents in managed and tidal wetlands over 5 years, and used capture-mark-recapture analyses to estimate demographic parameters and abundance for the three most common rodents—the northern SMHM (R. r. halicoetes), the western harvest mouse (a sympatric native species; R. megalotis, WHM), and the house mouse (a sympatric invasive species; Mus musculus). Wetland type had no effect on detection, temporary emigration, or survival for any of these species. However, fecundity and population growth for all three species were affected by an interaction of season and wetland type, although none of these parameters was consistently superior in either habitat type. Estimated abundance of SMHM and Mus was similar in both wetland types, whereas WHM were more abundant in managed wetlands. Salt marsh harvest mice also showed no affinity for any microhabitat characteristics associated with tidal wetlands. Managed wetlands in Suisun Marsh support SMHM and Mus equally, and abundances of WHM were greater than in tidal wetlands, suggesting managed wetlands may be superior in terms of supporting native rodents. As climate change and sea level rise are predicted to threaten coastal marshes, these results suggest the recovery strategy for SMHM could incorporate managed wetlands.

Estimating population parameters for the Critically Endangered Bermuda skink using robust design capture–mark–recapture modelling

Reliably estimating population parameters for highly secretive or rare animals is challenging. We report on the status of the two largest remaining populations of the Critically Endangered Bermuda skink Plestiodon longirostris, using a robust design capture–mark–recapture analysis. Skinks were tagged with passive integrated transponders on two islands and captured on 15 sampling occasions per year over 3 years. The models provided precise estimates of abundance, capture and survival probabilities and temporary emigration. We estimated skink abundance to be 547 ± SE 63.5 on Southampton Island and 277 ± SE 28.4 on Castle Island. The populations do not appear to be stable and fluctuated at both sites over the 3-year period. Although the populations on these two islands appear viable, the Bermuda skink faces population fluctuations and remains threatened by increasing anthropogenic activities, invasive species and habitat loss. We recommend these two populations for continued monitoring and conservation efforts.

Full-annual demography and seasonal cycles in a resident vertebrate

Demography is usually studied at a single point in time within a year when species, mostly long-distance migrants, are more active and easier to find. However, this provides only a low-resolution glimpse into demographic temporal patterns, compromising a complete understanding of species’ population dynamics over full annual cycles. The full annual cycle is often influenced by environmental seasonality, which induces a cyclic behavior in many species. However, cycles have rarely been explicitly included in models for demographic parameters, and most information on full annual cycle demography is restricted to migratory species. Here we used a high-resolution capture-recapture study of a resident tropical lizard to assess the full intra-annual demography and within-year periodicity in survival, temporary emigration and recapture probabilities. We found important variation over the annual cycle and up to 92% of the total monthly variation explained by cycles. Fine-scale demographic studies and assessments on the importance of cycles within parameters are fundamental to understand population persistence over time.