Relation between Occupancy and Abundance for a Territorial Species,the California Spotted Owl

Land and resource managers often use detection–nondetection surveys to monitor the populations of species that may be affected by factors such as habitat alteration, climate change, and biological invasions. Relative to mark‐recapture studies, using detection–nondetection surveys is more cost‐effective, and recent advances in statistical analyses allow the incorporation of detection probability, covariates, and multiple seasons. We examined the efficacy of using detection–nondetection data (relative to mark‐recapture data) for monitoring population trends of a territorial species, the California Spotted Owl (Strix occidentalis occidentalis). We estimated and compared the finite annual rates of population change (λ_t) and the resulting realized population change (Δ_t) from both occupancy and mark‐recapture data collected over 18 years (1993–2010). We used multiseason, robust‐design occupancy models to estimate that territory occupancy declined during our study (Δ_t = 0.702, 95% CI 0.552–0.852) due to increasing territory extinction rates ( = 0.019 [SE 0.012]; = 0.134 [SE 0.043]) and decreasing colonization rates ( = 0.323 [SE 0.124]; = 0.242 [SE 0.058]). We used Pradel's temporal‐symmetry model for mark‐recapture data to estimate that the population trajectory closely matched the trends in territory occupancy (Δ_t = 0.725, 95% CI 0.445–1.004). Individual survival was constant during our study ( = 0.816 [SE 0.020]; = 0.815 [SE 0.019]), whereas recruitment declined slightly ( = 0.195 [SE 0.032]; = 0.160 [SE 0.023]). Thus, we concluded that detection–nondetection data can provide reliable inferences on population trends, especially when funds preclude more intensive mark‐recapture studies. Relación entre Ocupación y Abundancia en una Especie Territorial, el Búho Moteado de California     

Revealing life‐history traits by contrasting genetic estimations with predictions of effective population size

Effective population size, a central concept in conservation biology, is now routinely estimated from genetic surveys and can also be theoretically predicted from demographic, life‐history, and mating‐system data. By evaluating the consistency of theoretical predictions with empirically estimated effective size, insights can be gained regarding life‐history characteristics and the relative impact of different life‐history traits on genetic drift. These insights can be used to design and inform management strategies aimed at increasing effective population size. We demonstrated this approach by addressing the conservation of a reintroduced population of Asiatic wild ass (Equus hemionus). We estimated the variance effective size (N_ev) from genetic data () and formulated predictions for the impacts on N_ev of demography, polygyny, female variance in lifetime reproductive success (RS), and heritability of female RS. By contrasting the genetic estimation with theoretical predictions, we found that polygyny was the strongest factor affecting genetic drift because only when accounting for polygyny were predictions consistent with the genetically measured N_ev. The comparison of effective‐size estimation and predictions indicated that 10.6% of the males mated per generation when heritability of female RS was unaccounted for (polygyny responsible for 81% decrease in N_ev) and 19.5% mated when female RS was accounted for (polygyny responsible for 67% decrease in N_ev). Heritability of female RS also affected N_ev; (heritability responsible for 41% decrease in N_ev). The low effective size is of concern, and we suggest that management actions focus on factors identified as strongly affecting , namely, increasing the availability of artificial water sources to increase number of dominant males contributing to the gene pool. This approach, evaluating life‐history hypotheses in light of their impact on effective population size, and contrasting predictions with genetic measurements, is a general, applicable strategy that can be used to inform conservation practice.     

Occupancy Patterns of Regionally Declining Grassland Sparrow Populations in a Forested Pennsylvania Landscape

Organisms can be affected by processes in the surrounding landscape outside the boundary of habitat areas and by local vegetation characteristics. There is substantial interest in understanding how these processes affect populations of grassland birds, which have experienced substantial population declines. Much of our knowledge regarding patterns of occupancy and density stem from prairie systems, whereas relatively little is known regarding how occurrence and abundance of grassland birds vary in reclaimed surface mine grasslands. Using distance sampling and single‐season occupancy models, we investigated how the occupancy probability of Grasshopper (Ammodramus savannarum) and Henslow's Sparrows (A. henslowii) on 61 surface mine grasslands (1591 ha) in Pennsylvania changed from 2002 through 2011 in response to landscape, grassland, and local vegetation characteristics . A subset (n = 23; 784 ha) of those grasslands were surveyed in 2002, and we estimated changes in sparrow density and vegetation across 10 years. Grasshopper and Henslow's Sparrow populations declined 72% and 49%, respectively from 2002 to 2011, whereas overall woody vegetation density increased 2.6 fold. Henslow's Sparrows avoided grasslands with perimeter–area ratios ≥0.141 km/ha and woody shrub densities ≥0.04 shrubs/m². Both species occupied grasslands ≤13 ha, but occupancy probability declined with increasing grassland perimeter–area ratio and woody shrub density. Grassland size, proximity to nearest neighboring grassland ( = 0.2 km), and surrounding landscape composition at 0.5, 1.5, and 3.0 km were not parsimonious predictors of occupancy probability for either species. Our results suggest that reclaimed surface mine grasslands, without management intervention, are ephemeral habitats for Grasshopper and Henslow's Sparrows. Given the forecasted decline in surface coal production for Pennsylvania, it is likely that both species will continue to decline in our study region for the foreseeable future. Patrones de Ocupación de Poblaciones Regionalmente Declinantes de Gorriones de Pastizales en un Paisaje Boscoso de Pennsylvania     

Using ensemble modeling to predict the impacts of assisted migration on recipient ecosystems

Assisted migration is a controversial conservation measure that aims to protect threatened species by moving part of their population outside its natural range. Although this could save species from extinction, it also introduces a range of risks. The magnitude of the threat to recipient ecosystems has not been investigated quantitatively, despite being the most common criticism leveled at the action. We used an ensemble modeling framework to estimate the risks of assisted migration to existing species within ecosystems. With this approach, we calculated the consequences of an assisted migration project across a very large combination of translocated species and recipient ecosystems. We predicted the probability of a successful assisted migration and the number of local extinctions would result from establishment of the translocated species. Using an ensemble of simulated 15-species recipient ecosystems, we estimated that translocated species will successfully establish in 83% of cases if introduced to stable, high-quality habitats. However, assisted migration projects were estimated to cause an average of 0.6 extinctions and 5% of successful translocations triggered 4 or more local extinctions. Quantifying the impacts to species within recipient ecosystems is critical to help managers weigh the benefits and negative consequences of assisted migration.     

Using long-term data for a reintroduced population to empirically estimate future consequences of inbreeding

Inbreeding depression is an important long-term threat to reintroduced populations. However, the strength of inbreeding depression is difficult to estimate in wild populations because pedigree data are inevitably incomplete and because good data are needed on survival and reproduction. Predicting future population consequences is especially difficult because this also requires projecting future inbreeding levels and their impacts on long-term population dynamics, which are subject to many uncertainties. We illustrate how such projections can be derived through Bayesian state-space modeling methods based on a 26-year data set for North Island Robins (Petroica longipes) reintroduced to Tiritiri Matangi Island in 1992. We used pedigree data to model increases in the average inbreeding level (F ) over time based on kinship of possible breeding pairs and to estimate empirically N_e/N (effective/census population size). We used multiple imputation to model the unknown components of inbreeding coefficients, which allowed us to estimate effects of inbreeding on survival for all 1458 birds in the data set while modeling density dependence and environmental stochasticity. This modeling indicated that inbreeding reduced juvenile survival (1.83 lethal equivalents [SE 0.81]) and may have reduced subsequent adult survival (0.44 lethal equivalents [0.81]) but had no apparent effect on numbers of fledglings produced. Average inbreeding level increased to 0.10 (SE 0.001) as the population grew from 33 (0.3) to 160 (6) individuals over the 25 years, giving a ratio of 0.56 (0.01). Based on a model that also incorporated habitat regeneration, the population was projected to reach a maximum of 331–1144 birds (median 726) in 2130, then to begin a slow decline. Without inbreeding, the population would be expected stabilize at 887–1465 birds (median 1131). Such analysis, therefore, makes it possible to empirically derive the information needed for rational decisions about inbreeding management while accounting for multiple sources of uncertainty.     

Range‐Wide Genetic Connectivity of the Hawaiian Monk Seal and Implications for Translocation

Abstract: The Hawaiian monk seal (Monachus schauinslandi) is one of the most critically endangered marine mammals. Less than 1200 individuals remain, and the species is declining at a rate of approximately 4% per year as a result of juvenile starvation, shark predation, and entanglement in marine debris. Some of these problems may be alleviated by translocation; however, if island breeding aggregates are effectively isolated subpopulations, moving individuals may disrupt local adaptations. In these circumstances, managers must balance the pragmatic need of increasing survival with theoretical concerns about genetic viability. To assess range‐wide population structure of the Hawaiian monk seal, we examined an unprecedented, near‐complete genetic inventory of the species (n =1897 seals, sampled over 14 years) at 18 microsatellite loci. Genetic variation was not spatially partitioned (_w=?0.03, p = 1.0), and a Bayesian clustering method provided evidence of one panmictic population (K =1). Pairwise F_ST comparisons (among 7 island aggregates over 14 annual cohorts) did not reveal temporally stable, spatial reproductive isolation. Our results coupled with long‐term tag‐resight data confirm seal movement and gene flow throughout the Hawaiian Archipelago. Thus, human‐mediated translocation of seals among locations is not likely to result in genetic incompatibilities.     

Sea-Cage Aquaculture, Sea Lice, and Declines of Wild Fish

Abstract: A sea cage, sometimes referred to as a net pen, is an enclosure designed to prevent farm fish from escaping and to protect them from large predators, while allowing a free flow of water through the cage to carry away waste. Farm fish thus share water with wild fish, which enables transmission of parasites, such as sea lice, from wild to farm and farm to wild fishes. Sea lice epidemics, together with recently documented population‐level declines of wild salmon in areas of sea‐cage farming, are a reminder that sea‐cage aquaculture is fundamentally different from terrestrial animal culture. The difference is that sea cages protect farm fish from the usual pathogen‐control mechanisms of nature, such as predators, but not from the pathogens themselves. A sea cage thus becomes an unintended pathogen factory. Basic physical theory explains why sea‐cage aquaculture causes sea lice on sympatric wild fish to increase and why increased lice burdens cause wild fish to decline, with extirpation as a real possibility. Theory is important to this issue because slow declines of wild fish can be difficult to detect amid large fluctuations from other causes. The important theoretical concepts are equilibrium, host‐density effect, reservoir‐host effect, and critical stocking level of farmed fish (stocking level at which lice proliferate on farm fish even if wild fish are not present to infect them). I explored these concepts and their implications without mathematics through examples from salmon farming. I also considered whether the lice‐control techniques used by sea‐cage farmers (medication and shortened grow‐out times) are capable of protecting wild fish. Elementary probability showed that (where W is the abundance of wild fish, W* is the prefarm abundance, F is the abundance of farm fish, and is the ratio of lice per farm fish to lice per wild fish). Declines of wild fish can be reduced by short growing cycles for farm fish, medicating farm fish, and keeping farm stocking levels low. Declines can be avoided only by ensuring that wild fish do not share water with farmed fish, either by locating sea cages very far from wild fish or through the use of closed‐containment aquaculture systems. These principles are likely to govern any aquaculture system where cage‐protected farm hosts and sympatric wild hosts have a common parasite with a direct life cycle.     

Changes in Avian and Plant Communities of Aspen Woodlands over 12 Years after Livestock Removal in the Northwestern Great Basin

Abstract: Riparian and quaking aspen (Populus tremuloides) woodlands are centers of avian abundance and diversity in the western United States, but they have been affected adversely by land use practices, particularly livestock grazing. In 1990, cattle were removed from a 112,500‐ha national wildlife refuge in southeastern Oregon. Thereafter, we monitored changes in vegetation and bird abundance in years 1–3 (phase 1) and 10–12 (phase 2) in 17 riparian and 9 snow‐pocket aspen plots. On each 1.5‐ha plot, we sampled vegetation in 6 transects. Three times during each breeding season, observers recorded all birds 50 m to each side of the plot's 150‐m centerline for 25 minutes. We analyzed data with multivariate analysis of variance and paired t tests with p values adjusted for multiple comparisons. In both periods, riparian and snow‐pocket aspen produced extensive regeneration of new shoots ( stems/ha and 7079 stems/ha, respectively). By phase 2, a 64% increase in medium‐diameter trees in riparian stands indicated successful recruitment into the overstory, but this pattern was not seen in snow‐pocket stands, where the density of trees was over 2 times greater. By phase 2 in riparian and snow‐pocket stands, native forb cover had increased by 68% and 57%, respectively, mesic shrub cover had increased by 29% and 58%, and sagebrush cover had decreased by 24% and 31%. Total avian abundance increased by 33% and 39% in riparian and snow‐pocket aspen, respectively, ground or understory nesters increased by 133% and 67% and overstory nesters increased by 34% and 33%. Similarly, ground or understory foragers increased by 25% and 32%, aerial foragers by 55% and 57%, and overstory foragers by 66% and 43%. We interpreted the substantial regeneration of aspen shoots, increased densities of riparian forbs and shrubs, and increased avian abundances as a multitrophic‐level response to the total removal of livestock and as substantial movement toward recovery of biological integrity.     

Generation of Priority Research Questions to Inform Conservation Policy and Management at a National Level

Abstract: Integrating knowledge from across the natural and social sciences is necessary to effectively address societal tradeoffs between human use of biological diversity and its preservation. Collaborative processes can change the ways decision makers think about scientific evidence, enhance levels of mutual trust and credibility, and advance the conservation policy discourse. Canada has responsibility for a large fraction of some major ecosystems, such as boreal forests, Arctic tundra, wetlands, and temperate and Arctic oceans. Stressors to biological diversity within these ecosystems arise from activities of the country's resource‐based economy, as well as external drivers of environmental change. Effective management is complicated by incongruence between ecological and political boundaries and conflicting perspectives on social and economic goals. Many knowledge gaps about stressors and their management might be reduced through targeted, timely research. We identify 40 questions that, if addressed or answered, would advance research that has a high probability of supporting development of effective policies and management strategies for species, ecosystems, and ecological processes in Canada. A total of 396 candidate questions drawn from natural and social science disciplines were contributed by individuals with diverse organizational affiliations. These were collaboratively winnowed to 40 by our team of collaborators. The questions emphasize understanding ecosystems, the effects and mitigation of climate change, coordinating governance and management efforts across multiple jurisdictions, and examining relations between conservation policy and the social and economic well‐being of Aboriginal peoples. The questions we identified provide potential links between evidence from the conservation sciences and formulation of policies for conservation and resource management. Our collaborative process of communication and engagement between scientists and decision makers for generating and prioritizing research questions at a national level could be a model for similar efforts beyond Canada.     

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.     

Seasonal photosynthetic characteristics of Ascoseira mirabilis (Ascoseirales,Phaeophyceae) from King George Island,Antarctica

Monthly variation in photosynthesis, dark respiration, chlorophyll a content and carbon: nitrogen (C:N) ratios in different lamina sections of adult plants of Ascoseira mirabilis Skottsberg from King George Island, Antarctica, was investigated between September 1993 and February 1994. Light saturated net photosynthesis (P _max) showed maximum values in September (12 to 25 mol O₂ g^-1 fr wt h^-1), and decreased towards the summer to values ranging between 2.0 and 5.0 mol O₂ g^-1. In the distal section, however, a second optimum occurred in December (25 mol O₂ g^-1 fr wt h^-1). Dark respiration rates were also highest in October and November and decreased strongly in December to February (6.0 and 1.0 mol O₂ g^-1 fr wt h^-1, respectively). Gross photosynthesis exhibited high values between September and December. Concomitant with the seasonal decrease of photosynthetic efficiency () from mean values of 1.2 mol O₂ g^-1 fr wt h^-1 (mol photons cm^-2 s^-1)^-1 in September to 0.3 mol O₂ g^-1 fr wt h^-1 (mol photons cm^-2 s^-1)^-1 in January, the initial light saturating point (I _k) gradually increased from 19 to 60 mol photons m^-2 s^-1. Likewise C:N ratios were low in spring (12 to 13) and increased in summer (20). In general, the photosynthetic parameters P _max, gross photosynthesis, and Chl a concentrations were significantly higher in the distal section of the thallus. In contrast, C:N ratios were lower in the distal section of the lamina. The results show that photosynthesis obviously strongly supports growth of the alga in late winter to spring, as it does in some morphologically related brown algae from temperate and polar regions. The question whether growth is additionally powered     

Stable isotope and biochemical fractionation in the marine pelagic food chain: the jellyfish Pelagia noctiluca and net zooplankton

In our field study we analyzed the C and H isotopic and biochemical (C, N, P, protein, lipid, carbohydrate) composition of the jellyfish Pelagia noctiluca (collected from the Gulf of Trieste in 1985 to 1986) and its presumed diet-net zooplankton. The mean ¹³C (-18.8) and D (-58.4) ratios of P. noctiluca showed enrichment in heavy isotopes relative to net zooplankton (2 for carbon and 30 for hydrogen). Both the jellyfish and net zooplankton were characterized by a linear correlation between ¹³C and D. C. N, P, protein, lipid, and carbohydrate contents of P. noctiluca were low on a dry weight basis as compared to net zooplankton. Significantly lower C:N and C:P ratios were found in jellyfish indicating a greater loss of carbon relative to nitrogen and phosphorus along the passage to a higher trophic level. Isotopic and biochemical evidence indicate that, though collected in nearshore waters, P. noctiluca depended on autochthonous marine organic matter.     

Autotoxic antibiotic production by a marine Chromobacterium

An antibiotic-producing Chromobacter was isolated from a sea-water sample from the North Pacific Gyre. The bacterium produces 3 bromine-containing metabolites: tetrabromopyrrole, 2-(2-hydroxy-3, 5-dibromophenyl)-3, 4, 5-tribromopyrrole, and hexabromo-2, 2-bipyrrole. It also synthesizes n-propyl 4-hydroxybenzoate and 4-hydroxybenzaldehyde. Some of these compounds were shown to be responsible for autoinhibition of the Chromobacterium itself, as well as for antibiotic action against other kinds of bacteria.     

A syntrophic propionate-oxidizing microflora and its bioaugmentation on anaerobic wastewater treatment for enhancing methane production and COD removal

Methane fermentation process can be restricted and even destroyed by the accumulation of propionate because it is the most difficult to be anaerobically oxidized among the volatile fatty acids produced by acetogenesis. To enhance anaerobic wastewater treatment process for methane production and COD removal, a syntrophic propionate-oxidizing microflora B83 was obtained from an anaerobic activated sludge by enrichment with propionate. The inoculation of microflora B83, with a 1:9 ratio of bacteria number to that of the activated sludge, could enhance the methane production from glucose by 2.5 times. With the same inoculation dosage of the microflora B83, COD removal in organic wastewater treatment process was improved from 75.6% to 86.6%, while the specific methane production by COD removal was increased by 2.7 times. Hydrogen-producing acetogenesis appeared to be a rate-limiting step in methane fermentation, and the enhancement of hydrogen-producing acetogens in the anaerobic wastewater treatment process had improved not only the hydrogen-producing acetogenesis but also the acidogenesis and methanogenesis.

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