Dealing with the Clandestine Nature of Wildlife‐Trade Market Surveys

Abstract: Illegal international trade in wildlife (excluding fisheries and timber) has been valued at more than US$20 billion. A more precise figure has not been determined in part because of the clandestine nature of the trade, and for this same reason even regional and local levels of wildlife trade are difficult to assess. The application of recent developments in wildlife field‐survey methods (e.g., occupancy) now allows for a more‐accurate estimation of wildlife trade occurrence, including its hidden components at a variety of scales (e.g., regional, local) and periods (e.g., single season, 1 year, multiple years). Occupancy models have been applied in wildlife field studies to address the problem of false absences when conducting presence–absence surveys. Occupancy surveys differ from traditional presence–absence surveys because they incorporate repeat surveys, allowing for the likelihood of detecting a species (the probability of detection) to be estimated explicitly (in contrast to traditional surveys that often incorrectly treat this probability as close to one to allow for estimation of presence). Occupancy methods can be applied to a variety of wildlife‐trade surveys, including, for example, single‐species availability, links between two illegally traded species (i.e., co‐occurrence), and disease occurrence in live trade. In addition, free user‐friendly software (i.e., PRESENCE) allows even nonstatisticians to adequately address this issue. I simulated a hypothetical wildlife‐trade market survey that resulted in an apparent 20% decline in naïve occupancy (proportion of surveyed towns engaged in the trade) over 2 years, but when I accounted for change in probability of detection over the years the difference in occupancy was not statistically significant. As more sophisticated methods, such as occupancy, are applied to wildlife‐trade market surveys, results will be more robust and defensible and therefore, theoretically, more powerful when presented to conservation policy and decision makers.     

Breeding Periodicity for Male Sea Turtles,Operational Sex Ratios,and Implications in the Face of Climate Change

Abstract: Species that have temperature‐dependent sex determination (TSD) often produce highly skewed offspring sex ratios contrary to long‐standing theoretical predictions. This ecological enigma has provoked concern that climate change may induce the production of single‐sex generations and hence lead to population extirpation. All species of sea turtles exhibit TSD, many are already endangered, and most already produce sex ratios skewed to the sex produced at warmer temperatures (females). We tracked male loggerhead turtles (Caretta caretta) from Zakynthos, Greece, throughout the entire interval between successive breeding seasons and identified individuals on their breeding grounds, using photoidentification, to determine breeding periodicity and operational sex ratios. Males returned to breed at least twice as frequently as females. We estimated that the hatchling sex ratio of 70:30 female to male for this rookery will translate into an overall operational sex ratio (OSR) (i.e., ratio of total number of males vs females breeding each year) of close to 50:50 female to male. We followed three male turtles for between 10 and 12 months during which time they all traveled back to the breeding grounds. Flipper tagging revealed the proportion of females returning to nest after intervals of 1, 2, 3, and 4 years were 0.21, 0.38, 0.29, and 0.12, respectively (mean interval 2.3 years). A further nine male turtles were tracked for short periods to determine their departure date from the breeding grounds. These departure dates were combined with a photoidentification data set of 165 individuals identified on in‐water transect surveys at the start of the breeding season to develop a statistical model of the population dynamics. This model produced a maximum likelihood estimate that males visit the breeding site 2.6 times more often than females (95%CI 2.1, 3.1), which was consistent with the data from satellite tracking and flipper tagging. Increased frequency of male breeding will help ameliorate female‐biased hatchling sex ratios. Combined with the ability of males to fertilize the eggs of many females and for females to store sperm to fertilize many clutches, our results imply that effects of climate change on the viability of sea turtle populations are likely to be less acute than previously suspected.     

Population Bottlenecks and Increased Hatching Failure in Endangered Birds

Abstract: Severe population bottlenecks are expected to lead to increases in inbreeding depression and to reduce the long‐term viability of populations. We compared hatching failure across 51 threatened bird species to test the relation between the size of population bottleneck and population viability. Bottleneck size was defined as the lowest population size recorded in a species. Hatching failure was estimated as the proportion of eggs that failed to hatch due to infertility and embryonic death, both of which increase with inbreeding. The size of the bottleneck varied from 4 to 20,000 individuals across species and had a significant negative effect on hatching failure, a pattern that was consistent when we controlled for the confounding effects of phylogeny, body size, clutch size, time since the bottleneck occurred, and latitude. Hatching failure varied from 3 to 64% across species and was more than 10% in all populations passing through bottlenecks below 100–150 individuals. Our results show that the negative consequences of bottlenecks on hatching success are widespread in the populations of species we examined, and emphasize the conservation benefit of preventing bottlenecks below 150 individuals.     

Scientific Gear as a Vector for Non-Native Species at Deep-Sea Hydrothermal Vents

The fauna of deep-sea hydrothermal vents are among the most isolated and inaccessible biological communities on Earth. Most vent sites can only be visited by subsea vehicles, which can and do move freely among these communities. Researchers assume individuals of the regionally homogeneous vent fauna are killed by the change in hydrostatic pressure the animals experience when the subsea vehicles, which collected them, rise to the surface. After an Alvin dive, we found 38 apparently healthy individuals of a vent limpet in a sample from a hydrothermally inactive area. Prompted by our identification of these specimens as Lepetodrilus gordensis, a species restricted to vents 635 km to the south of our dive site, we tested whether they were from a novel population or were contaminants from the dive made 36 h earlier. The 16S gene sequences, morphology, sex ratio, bacterial colonies, and stable isotopes uniformly indicated the specimens came from the previous dive. We cleaned the sampler, but assumed pressure changes would kill any organisms we did not remove and that the faunas of the 2 areas were nearly identical and disease-free. Our failure to completely clean the gear on the subsea vehicle meant we could have introduced the species and any diseases it carried to a novel location. Our findings suggest that the nearly inaccessible biological communities at deep-sea vents may be vulnerable to anthropogenic alteration, despite their extreme physical conditions.     

Specimen‐Based Modeling,Stopping Rules,and the Extinction of the Ivory‐Billed Woodpecker

Abstract: Assessing species survival status is an essential component of conservation programs. We devised a new statistical method for estimating the probability of species persistence from the temporal sequence of collection dates of museum specimens. To complement this approach, we developed quantitative stopping rules for terminating the search for missing or allegedly extinct species. These stopping rules are based on survey data for counts of co‐occurring species that are encountered in the search for a target species. We illustrate both these methods with a case study of the Ivory‐billed Woodpecker (Campephilus principalis), long assumed to have become extinct in the United States in the 1950s, but reportedly rediscovered in 2004. We analyzed the temporal pattern of the collection dates of 239 geo‐referenced museum specimens collected throughout the southeastern United States from 1853 to 1932 and estimated the probability of persistence in 2011 as <6.4 × 10^?5, with a probable extinction date no later than 1980. From an analysis of avian census data (counts of individuals) at 4 sites where searches for the woodpecker were conducted since 2004, we estimated that at most 1–3 undetected species may remain in 3 sites (one each in Louisiana, Mississippi, Florida). At a fourth site on the Congaree River (South Carolina), no singletons (species represented by one observation) remained after 15,500 counts of individual birds, indicating that the number of species already recorded (56) is unlikely to increase with additional survey effort. Collectively, these results suggest there is virtually no chance the Ivory‐billed Woodpecker is currently extant within its historical range in the southeastern United States. The results also suggest conservation resources devoted to its rediscovery and recovery could be better allocated to other species. The methods we describe for estimating species extinction dates and the probability of persistence are generally applicable to other species for which sufficient museum collections and field census results are available.     

Selecting for Tolerance against Pathogens and Herbivores to Enhance Success of Reintroduction and Translocation

Abstract: Some species have insufficient defenses against climate change, emerging infectious diseases, and non‐native species because they have not been exposed to these factors over their evolutionary history, and this can decrease their likelihood of persistence. Captive breeding programs are sometimes used to reintroduce individuals back into the wild; however, successful captive breeding and reintroduction can be difficult because species or populations often cannot coexist with non‐native pathogens and herbivores without artificial selection. In captive breeding programs, breeders can select for host defenses that prevent or reduce pathogen or herbivore burden (i.e., resistance) or traits that limit the effects of parasitism or herbivory on host fitness (i.e., tolerance). We propose that selection for host tolerance may enhance the success of reintroduction or translocation because tolerant hosts generally have neutral effects on introduced pathogens and herbivores. The release of resistant hosts would have detrimental effects on their natural enemies, promoting rapid evolution to circumvent the host resistance that may reduce the long‐term probability of persistence of the reintroduced or translocated species. We examined 2 case studies, one on the pathogenic amphibian chytrid fungus ( Batrachochytrium dendrobatidis [Bd]) and the other on the herbivorous cactus moth ( Cactoblastis cactorum) in the United States, where it is not native. In each case study, we provide recommendations for how captive breeders and managers could go about selecting for host tolerance. Selecting for tolerance may offer a promising tool to rescue hosts species from invasive natural enemies as well as new natural enemies associated with climate change‐induced range shifts.     

Potential Effects of Ongoing and Proposed Hydropower Development on Terrestrial Biological Diversity in the Indian Himalaya

Indian Himalayan basins are earmarked for widespread dam building, but aggregate effects of these dams on terrestrial ecosystems are unknown. We mapped distribution of 292 dams (under construction and proposed) and projected effects of these dams on terrestrial ecosystems under different scenarios of land‐cover loss. We analyzed land‐cover data of the Himalayan valleys, where dams are located. We estimated dam density on fifth‐ through seventh‐order rivers and compared these estimates with current global figures. We used a species–area relation model (SAR) to predict short‐ and long‐term species extinctions driven by deforestation. We used scatter plots and correlation studies to analyze distribution patterns of species and dams and to reveal potential overlap between species‐rich areas and dam sites. We investigated effects of disturbance on community structure of undisturbed forests. Nearly 90% of Indian Himalayan valleys would be affected by dam building and 27% of these dams would affect dense forests. Our model projected that 54,117 ha of forests would be submerged and 114,361 ha would be damaged by dam‐related activities. A dam density of 0.3247/1000 km² would be nearly 62 times greater than current average global figures; the average of 1 dam for every 32 km of river channel would be 1.5 times higher than figures reported for U.S. rivers. Our results show that most dams would be located in species‐rich areas of the Himalaya. The SAR model projected that by 2025, deforestation due to dam building would likely result in extinction of 22 angiosperm and 7 vertebrate taxa. Disturbance due to dam building would likely reduce tree species richness by 35%, tree density by 42%, and tree basal cover by 30% in dense forests. These results, combined with relatively weak national environmental impact assessment and implementation, point toward significant loss of species if all proposed dams in the Indian Himalaya are constructed. Efectos Potenciales del Desarrollo Hidroeléctrico Actual y Propuesto sobre la Diversidad Biológica Terrestre en el Himalaya Hindú     

Projected Climate‐Induced Habitat Loss for Salmonids in the John Day River Network,Oregon, U.S.A.

Abstract: Climate change will likely have profound effects on cold‐water species of freshwater fishes. As temperatures rise, cold‐water fish distributions may shift and contract in response. Predicting the effects of projected stream warming in stream networks is complicated by the generally poor correlation between water temperature and air temperature. Spatial dependencies in stream networks are complex because the geography of stream processes is governed by dimensions of flow direction and network structure. Therefore, forecasting climate‐driven range shifts of stream biota has lagged behind similar terrestrial modeling efforts. We predicted climate‐induced changes in summer thermal habitat for 3 cold‐water fish species—juvenile Chinook salmon, rainbow trout, and bull trout (Oncorhynchus tshawytscha, O. mykiss, and Salvelinus confluentus, respectively)—in the John Day River basin, northwestern United States. We used a spatially explicit statistical model designed to predict water temperature in stream networks on the basis of flow and spatial connectivity. The spatial distribution of stream temperature extremes during summers from 1993 through 2009 was largely governed by solar radiation and interannual extremes of air temperature. For a moderate climate change scenario, estimated declines by 2100 in the volume of habitat for Chinook salmon, rainbow trout, and bull trout were 69–95%, 51–87%, and 86–100%, respectively. Although some restoration strategies may be able to offset these projected effects, such forecasts point to how and where restoration and management efforts might focus.     

Effects of Private‐Land Use,Livestock Management,and Human Tolerance on Diversity,Distribution, and Abundance of Large African Mammals

Successful conservation of large terrestrial mammals (wildlife) on private lands requires that landowners be empowered to manage wildlife so that benefits outweigh the costs. Laikipia County, Kenya, is predominantly unfenced, and the land uses in the area allow wide‐ranging wildlife to move freely between different management systems on private land. We used camera traps to sample large mammals associated with 4 different management systems (rhinoceros sanctuaries, no livestock; conservancies, intermediate stocking level; fenced ranches, high stocking level; and group ranches, high stocking level, no fencing, pastoralist clan ownership) to examine whether management and stocking levels affect wildlife. We deployed cameras at 522 locations across 8 properties from January 2008 through October 2010 and used the photographs taken during this period to estimate richness, occupancy, and relative abundance of species. Species richness was highest in conservancies and sanctuaries and lowest on fenced and group ranches. Occupancy estimates were, on average, 2 and 5 times higher in sanctuaries and conservancies as on fenced and group ranches, respectively. Nineteen species on fenced ranches and 25 species on group ranches were considered uncommon (occupancy < 0.1). The relative abundance of most species was highest or second highest in sanctuaries and conservancies. Lack of rights to manage and utilize wildlife and uncertain land tenure dampen many owners’ incentives to tolerate wildlife. We suggest national conservation strategies consider landscape‐level approaches to land‐use planning that aim to increase conserved areas by providing landowners with incentives to tolerate wildlife. Possible incentives include improving access to ecotourism benefits, forging agreements to maintain wildlife habitat and corridors, resolving land‐ownership conflicts, restoring degraded rangelands, expanding opportunities for grazing leases, and allowing direct benefits to landowners through wildlife harvesting. Efectos del Uso Privado de Suelo, Manejo de Ganado y la Tolerancia Humana sobre la Diversidad, Distribución y Abundancia de Mamíferos Mayores Africanos     

Incorporating Uncertainty of Management Costs in Sensitivity Analyses of Matrix Population Models

The importance of accounting for economic costs when making environmental‐management decisions subject to resource constraints has been increasingly recognized in recent years. In contrast, uncertainty associated with such costs has often been ignored. We developed a method, on the basis of economic theory, that accounts for the uncertainty in population‐management decisions. We considered the case where, rather than taking fixed values, model parameters are random variables that represent the situation when parameters are not precisely known. Hence, the outcome is not precisely known either. Instead of maximizing the expected outcome, we maximized the probability of obtaining an outcome above a threshold of acceptability. We derived explicit analytical expressions for the optimal allocation and its associated probability, as a function of the threshold of acceptability, where the model parameters were distributed according to normal and uniform distributions. To illustrate our approach we revisited a previous study that incorporated cost‐efficiency analyses in management decisions that were based on perturbation analyses of matrix population models. Incorporating derivations from this study into our framework, we extended the model to address potential uncertainties. We then applied these results to 2 case studies: management of a Koala (Phascolarctos cinereus) population and conservation of an olive ridley sea turtle (Lepidochelys olivacea) population. For low aspirations, that is, when the threshold of acceptability is relatively low, the optimal strategy was obtained by diversifying the allocation of funds. Conversely, for high aspirations, the budget was directed toward management actions with the highest potential effect on the population. The exact optimal allocation was sensitive to the choice of uncertainty model. Our results highlight the importance of accounting for uncertainty when making decisions and suggest that more effort should be placed on understanding the distributional characteristics of such uncertainty. Our approach provides a tool to improve decision making.