John R. Skalski

Techniques for wildlife investigations : design and analysis of capture data

Statistical inference in experimentation use of preliminary survey data surveys of animal abundance comparative censuses manipulative experiments environmental assessment studies. Appendices: General variance component formula noncentral F-tables additional noncentral F-tables.

Survival Estimates for Migrant Yearling Chinook Salmon and Steelhead Tagged with Passive Integrated Transponders in the Lower Snake and Lower Columbia Rivers, 1993–1998

Abstract Precise, up-to-date survival estimates for salmonids that migrate through reservoirs, hydroelectric dams, and free-flowing sections of the Snake and Columbia rivers are essential to develop effective strategies for recovering depressed stocks. To provide this information, survival was estimated for yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss with passive integrated transponder (PIT) tags that migrated through Snake River dams and reservoirs from 1993 through 1998. A multiple-recapture model for single release groups was used to estimate survival from detections of PIT-tagged fish at dams. The stretch of river over which survival was estimated varied between years, depending on the release site, the number of dams with the capability to detect and rerelease PIT-tagged fish back to the river, the total number of fish marked, and the efficiency of detecting PIT-tagged fish at each dam. Precision of survival estimates varied with the number of fish PIT-tagged and released...

Estimating Survival and Migration Route Probabilities of Juvenile Chinook Salmon in the Sacramento–San Joaquin River Delta

Abstract Juvenile Chinook salmon Oncorhynchus tshawytscha emigrating from natal tributaries of the Sacramento River must negotiate the Sacramento–San Joaquin River Delta, a complex network of natural and man-made channels linking the Sacramento River with San Francisco Bay. Natural processes and water management actions affect the fractions of the population using the different migration routes through the delta and survival within those routes. However, estimating these demographic parameters is difficult using traditional mark–recapture techniques, which depend on the physical recapture of fish (e.g., coded wire tags). Thus, our goals were to (1) develop a mark–recapture model to explicitly estimate the survival and migration route probabilities for each of four migration routes through the delta, (2) link these route-specific probabilities to population-level survival, and (3) apply this model to the first available acoustic telemetry data of smolt migration through the delta. The point estimate of sur...

Determination of ecological scale

We suggest that ecological processes and physical characteristics possess an inherent scale at which the processes or characteristics occur over the landscape. We propose a conceptual spatial response model that describes the nature of this ecological scale. Based on the proposed spatial model, we suggest methods for estimating the size of study plots or transects and the distance between replicate plots needed to approach statistical independence. Using data on percent cover for Agropyron spicatum, a common arid-land bunchgrass, we demonstrated four relationships that should hold if the spatial response model is appropriate. These relationships are sample variance increases as functions of (1) transect segment length and (2) intersegment length (transect segment dispersal), and correlation decreases as functions of (3) intersegment length and (4) transect segment length. Based on evaluation of these four relationships, cover for A. spicatum is correlated over the landscape on a scale of 400 to 700 m, and a segment length of 64 to 128 m is most appropriate for measuring cover for this species.

Factors Associated with Travel Time and Survival of Migrant Yearling Chinook Salmon and Steelhead in the Lower Snake River

Abstract Simple and multiple linear regressions were used to evaluate factors associated with travel time and survival of yearling chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss migrating in the lower Snake River. Factors were release date and environmental variables measuring river discharge (flow), water temperature, and the percentage of total flow passed over spillways at dams. Data were collected from migrant salmonids tagged with passive integrated transponder (PIT) tags from 1995 through 1999. The greatest distance over which survival could be estimated during all 5 years was from the Lower Granite Dam tailrace to the McNary Dam tailrace (225 river km encompassing four dams and reservoirs). Release groups consisted of PIT-tagged fish leaving Lower Granite Dam daily. Data from more than 451,000 PIT-tagged yearling chinook salmon and 204,000 PIT-tagged steelhead were analyzed. For each daily group, indices of exposure to environmental factors were calculated as the average value for ...

Demographic Response of Mule Deer to Experimental Reduction of Coyotes and Mountain Lions in Southeastern Idaho

ABSTRACT Manipulating predator populations is often posed as a solution to depressed ungulate populations. However, predator—prey dynamics are complex and the effect on prey populations is often an interaction of predator life history, climate, prey density, and habitat quality. The effect of predator removal on ungulate and, more specifically, mule deer (Odocoileus hemionus) populations has not been adequately investigated at a management scale. We tested the efficacy of removing coyotes (Cams latrans) and mountain lions (Puma concolor) for increasing survival and population growth rate of mule deer in southeastern Idaho, USA, during 1997–2003. We assigned 8 game management units (GMUs) to treatments under a 2 × 2 factorial design (treatments of coyote removal and lion removal) with 2 replicates of each treatment or reference area combination. We used methods typically available to wildlife managers to achieve predator removals and a combination of extensive and intensive monitoring in these 8 GMUs to test the hypothesis that predator removal increased vital rates and population growth rate of mule deer. We determined effects of predator removal on survival and causes of mortality in 2 intensive study sites, one with coyote and mountain lion removal and one without. We also considered the effects of other variables on survival including lagomorph abundance and climatic conditions. In these 2 intensive study areas, we monitored with radiotelemetry 250 neonates, 284 6-month-old fawns, and 521 adult females. At the extensive scale, we monitored mule deer population trend and December fawn ratios with helicopter surveys. Coyote removal decreased neonate mortality only when deer were apparently needed as alternate prey, thus removal was more effective when lagomorph populations were reduced. The best mortality model of mule deer captured at 6 months of age included summer precipitation, winter precipitation, fawn mass, and mountain lion removal. Over-winter mortality of adult female mule deer decreased with removal of mountain lions. Precipitation variables were included in most competing mortality models for all age classes of mule deer. Mountain lion removal increased fawn ratios and our models predicted fawn ratios would increase 6% at average removal rates (3.53/1,000 km2) and 27% at maximum removal rates (14.18/1,000 km). Across our extensive set of 8 GMUs, coyote removal had no effect on December fawn ratios. We also detected no strong effect of coyote or mountain lion removal alone on mule deer population trend; the best population-growth-rate model included previous years mountain lion removal and winter severity, yet explained only 27% of the variance in population growth rate. Winter severity in the current and previous winter was the most important influence on mule deer population growth. The lack of response in fawn ratio or mule deer abundance to coyote reduction at this extensive (landscape) scale suggests that decreased neonate mortality due to coyote removal is partially compensatory. Annual removal of coyotes was not an effective method to increase mule deer populations in Idaho because coyote removal increased radiocollared neonate fawn survival only under particular combinations of prey densities and weather conditions, and the increase did not result in population growth. Coyote-removal programs targeted in areas where mortality of mule deer fawns is known to be additive and coyote-removal conditions are successful may influence mule deer population vital rates but likely will not change direction of population trend. Although mountain lion removal increased mule-deer survival and fawn ratios, we were unable to demonstrate significant changes in population trend with mountain lion removal. In conclusion, benefits of predator removal appear to be marginal and short term in southeastern Idaho and likely will not appreciably change long-term dynamics of mule deer populations in the intermountain west.

Correcting bias in survival estimation resulting from tag failure in acoustic and radiotelemetry studies

The high detection rates of acoustic- and radio-tagged fish greatly improve the ability of an investigator to obtain information on survival and movement of fish with fewer tags. The trade-off, though, is a greater dependence on the individual tag performance, as each tagged fish in a smaller study represents a greater proportion of the outcome. This reduction in release size, due to the increase in detection capability, places a greater emphasis on the need to accurately gauge the status of the tagged fish. Should a tag fail while a smolt is migrating through the study area, the release-recapture model cannot discern the difference between smolt death and tag failure. If the release-recapture models are not adjusted for the probability of tag failure, the estimates of smolt survival will therefore be negatively biased. This article presents a semiparametric approach for adjusting survival estimates from release-recapture studies for tag failure, and provides subsequent estimation of sampling variance and its contributing components.

Assessment of Barotrauma from Rapid Decompression of Depth-Acclimated Juvenile Chinook Salmon Bearing Radiotelemetry Transmitters

Abstract This study investigated the mortality of and injury to juvenile Chinook salmon Oncorhynchus tshawytscha exposed to simulated pressure changes associated with passage through a large Kaplan hydropower turbine. Mortality and injury varied depending on whether a fish was carrying a transmitter, the method of transmitter implantation, the depth of acclimation, and the size of the fish. Juvenile Chinook salmon implanted with radio transmitters were more likely than those without to die or sustain injuries during simulated turbine passage. Gastric transmitter implantation resulted in higher rates of injury and mortality than surgical implantation. Mortality and injury increased with increasing pressure of acclimation. Injuries were more common in subyearling fish than in yearling fish. Gas emboli in the gills and internal hemorrhaging were the major causes of mortality. Rupture of the swim bladder and emphysema in the fins were also common. This research makes clear that the exposure of juvenile Chinoo...

Statistical models for population reconstruction using age-at-harvest data

Statistical analyses based on maximum likelihood methods are presented to jointly estimate harvest rates, survival, recruitment, and population abundance from age-at-harvest data. To perform the population reconstruction from the age-at-harvest data, auxiliary field data and information on harvest reporting rates are required. The statistical methods permit tests of model assumptions, goodness-of-fit, and standard errors and confidence intervals for all estimated demographic parameters. We illustrate the methods using harvest data and radiotelemetry studies of elk (Cervus elaphus) from northern Idaho, USA, 1988-1993. We compare results with abundance estimates using an aerial sightability survey on the same herd. The maximum likelihood methods for age-at-harvest analysis provide a comprehensive framework for population reconstruction with abundance estimates comparable to field survey techniques.

Effectiveness of Scat-Detection Dogs in Determining Species Presence in a Tropical Savanna Landscape

Most protected areas are too small to sustain populations of wide-ranging mammals; thus, identification and conservation of high-quality habitat for those animals outside parks is often a high priority, particularly for regions where extensive land conversion is occurring. This is the case in the vicinity of Emas National Park, a small protected area in the Brazilian Cerrado. Over the last 40 years the native vegetation surrounding the park has been converted to agriculture, but the region still supports virtually all of the animals native to the area. We determined the effectiveness of scat-detection dogs in detecting presence of five species of mammals threatened with extinction by habitat loss: maned wolf (Chrysocyon brachyurus), puma (Puma concolor), jaguar (Panthera onca), giant anteater (Myrmecophaga tridactyla), and giant armadillo (Priodontes maximus). The probability of scat detection varied among the five species and among survey quadrats of different size, but was consistent across team, season, and year. The probability of occurrence, determined from the presence of scat, in a randomly selected site within the study area ranged from 0.14 for jaguars, which occur primarily in the forested areas of the park, to 0.91 for maned wolves, the most widely distributed species in our study area. Most occurrences of giant armadillos in the park were in open grasslands, but in the agricultural matrix they tended to occur in riparian woodlands. At least one target species occurred in every survey quadrat, and giant armadillos, jaguars, and maned wolves were more likely to be present in quadrats located inside than outside the park. The effort required for detection of scats was highest for the two felids. We were able to detect the presence for each of five wide-ranging species inside and outside the park and to assign occurrence probabilities to specific survey sites. Thus, scat dogs provide an effective survey tool for rare species even when accurate detection likelihoods are required. We believe the way we used scat-detection dogs to determine the presence of species can be applied to the detection of other mammalian species in other ecosystems.