Focal species are a critical component of conservation planning, along with representation of ecosystems, special elements and ecologically sustainable management. They warrant conservation attention because they are functionally important, wide-ranging or space-demanding, habitat-quality indicators, ‘flagship’, and/or vulnerable or special populations. A delphi survey matrix-based approach, involving regional experts in the selection of potential focal species, was applied in Nova Scotia, Canada and Maine, USA. Matrices with native species on one axis and selection characteristics on the other axis were used to summarize expert knowledge and judgment. Characteristics were related to biological traits and habitat requirements that make some species more vulnerable than others in human-modified landscapes. In Nova Scotia and Maine, 19 and 11 experts, respectively, completed the matrices, which were subsequently numerically assessed. Species with the highest scores were identified as potential focal species, including wolf, cougar, lynx, river otter, eastern pipistrelle, wood turtle, four-toed salamander, golden eagle and Atlantic salmon. Concerns remain around the lack of representation of some classes of species, subjectivity in selecting and weighting characteristics, and the relative nature of assessing species against the characteristics. Accordingly, potential focal species should be subject to verification through more rigorous and quantitative analysis and monitoring. Nonetheless, if applied with care, the matrix-based approach can provide a relatively systematic and effective way of engaging regional experts in focal species selection.

The Galápagos Islands, a world heritage region for the protection of the unique terrestrial and marine wildlife, are also home to a small human population, dependent on fisheries. There was a lucrative sea-cucumber (Stichopus fuscus) fishery in the islands, which began in 1992. After a rapid expansion in the Galápagos archipelago, the fishery has declined and now persists predominantly around the western islands. Initially, the fishery was largely illegal and uncontrollable. Subsequently, a co-management framework developed, with fisher participation. Gradually enforcement improved, apparent corruption declined, and research capacity increased. Although stock abundance surveys have been carried out annually since 1993, the paucity of background biological and fishery information does not allow rigorous stock assessment. The achievements of co-management through the participation of fishers in research and management have been: an acceptance of management controls on numbers of fishers and quotas, a reduction in conflict and increased co-operation. Persistent problems have been: weak enforcement capacity, limited funds for patrolling and research, corruption and declining stock abundance. Proposed application of precautionary principles to management, including a range of fishery indicators, may save the fishery from collapse. The principles are applicable to many other data-poor fisheries globally.

Sampling scale and lack of attention to taxa other than scleractinian corals have limited the capacity to protect coral reefs and coral communities in Pacific Panama. The distribution of coral habitats (live coral cover) and their species richness in the largest marine protected area of Panama, the Coiba National Park (270 125 ha), is described using quadrat transects and manta tows. The species richness of scleractinian corals and octocorals was lower in coral reefs than in coral communities, and a close relationship between richness and live coral cover was observed only in coral communities. The distribution of high live coral cover in coral communities overlapped with areas of high coral species richness. Average live coral cover in communities was 64%, compared to 28% in reefs, whereas algae cover was 30% and 49%, respectively. Twenty-two coral and 34 octocoral species were observed, many only now detected in Panama as endemic or new species. Analysis of satellite imagery showed 80% of terrestrial habitats were mostly primary forest, and coral reefs and coral communities covered 1700 ha, about 2% of marine habitats. Shallow marine environments (< 20 m) had up to 60% calcareous red algae cover (rhodolite beds). Based on the distribution of live coral cover and species richness, three conservation units were identified as priority, with the southern and northernmost sides of the marine protected area as the most significant. These three areas encompass most of the rare and endemic species or populations, as well as species previously regarded as endangered.

The Saimaa ringed seal (Phoca hispida saimensis) is the only endemic mammal in Finland. At present the total population size of this subspecies is c. 250 individuals. Because the seal feeds on fish, and because of its value particularly as a source of meat, oil and leather, hunting was allowed until 1955. Conservation of the seal and some of its lairing areas by means of fishing restrictions requires the adoption of new attitudes. Semi-structured interviews elucidated the basis of conflicts concerning protection of the Saimaa ringed seal and fishing in Lake Pihlajavesi, Finland, where one of the most viable populations of the seal lives. Socio-economic position largely determined personal attitudes towards conservation; local landowners felt that their use of natural resources was restricted, while summer cottage owners wanted strict conservation. Commercial fishers considered the protection of the ringed seal unnecessary and a waste of money. Conservation biologists believed that the proposed actions were necessary to reduce the risk of extinction. Attitudes were also widely influenced by culture and social backgrounds. Those influenced by the traditional Finnish peasant/nature relationship had a different vision of nature from the conservationists who were influenced by modern science. Questions raised by the protection of the Saimaa ringed seal form an example of transition of an environmental conflict to larger-scale criticism of ongoing structural transformation in society. It is obvious that if nature conservation requires the approval of all social groups, it needs a change of authoritarian measures and acceptance of local knowledge, which should be used alongside scientific knowledge in management. Nature conservation policy led by specialists and authorities could be seen as widening the gap between urban and rural areas.

Spraying with the organophosphate fenthion has been the predominant means to control the red-billed quelea (Quelea quelea), a major bird pest throughout semi-arid regions of sub-Saharan Africa, for more than forty years. A review of known effects of fenthion and other control measures used against Q. quelea on non-target organisms, provides a basis for comparisons with any alternative chemical control agents. Birds of prey, owls and passerines have been commonly reported casualties of spraying with fenthion over land. Moreover, fenthion is known to have negative effects on aquatic invertebrates, in particular on populations of crustacea, which predicates against its use near water bodies. Non-target species may be affected directly by spraying, but predatory birds, scavenging birds and even mammals can be contaminated by secondary poisoning when they eat Quelea carcasses found up to 20 km or more from the primary control site. To avoid secondary poisoning, where possible quelea carcasses should be removed from a site after spraying. The use of explosions to kill roosting quelea birds has similar effects to those of fenthion in terrestrial habitats, killing non-target species including birds of prey and owls. Another control method, harvesting quelea as a source of protein, is benign and could contribute to local nutritional and economic needs. However harvesting is unlikely to reduce quelea populations substantially. Integrated pest management (IPM) approaches are recommended to minimize environmental damage, but until these are successfully adopted, standardized procedures for comparative assessments of the effects of quelea control are required.

Local user perceptions of resource trajectory and indicators of protected area outcomes can be useful in the assessment of integrated conservation projects, both marine and terrestrial. In-depth stakeholder surveys using 12 performance indicators were used to evaluate the perceived outcomes of the Sagay Marine Reserve (SMR), the Philippines. These indicators were a measure of whether the SMR had achieved its management objectives in the recent past and what local stakeholders expected in the future. The respondents' contextual situation could be correlated with their perceptions of SMR indicators. There was a generally high level of perceived equity and efficiency of SMR management outcomes, but the sustainability of the SMR, particularly the condition of the fisheries, had been poor over the previous 10 years. Few anticipated an improvement in sustainability indicators over the next 10 years. Respondents from an island village within the SMR had more negative (or less positive) perceptions of SMR outcomes because of their high dependence on the degraded resource, combined with physical and economic isolation. Specific remedies to enhance island villagers' satisfaction, such as greater participation, empowerment, alternative economic opportunities and fisheries protection, and replenishment, are necessary. This research serves as an example of how indicators perceived by local resource-accessing stakeholders can and should be main components of both marine and terrestrial protected area assessment.

The application of no-take marine reserve status to an area is expected to increase abundance and average size of individuals of species targeted by fisheries. The majority of the evidence supporting such expectations still involves comparisons of abundance at the one time of sites with and without marine reserve protection. Very few studies have data on the abundance and size structure of species targeted by fisheries in an area before reserve status is applied. Quantitative estimates of density and biomass of coral trout, Plectropomus spp., the major target of the hook and line fisheries on the Great Barrier Reef (GBR), Australia, on inshore fringing reefs of the Palm and Whitsunday Island groups, central GBR, are provided for 3–4 years before (1983–1984), and 12–13 years after (1999–2000) the establishment of no-take reserves in 1987. Quantitative estimates of density and biomass of coral trout in areas open to fishing were also collected in 1999–2000 at these two island groups. Density and biomass of coral trout increased significantly (by factors of 5.9 and 6.3 in the Palm Islands, and 4.0 and 6.2 in the Whitsunday Islands) in the reserve sites, but not the fished sites, between 1983–1984 and 1999–2000. In 1999–2000, density and biomass of coral trout and a secondary target of the fisheries, Lutjanus carponotatus, were significantly higher in the protected zones than in the fished zones at both island groups. The density and biomass of non-target fish species (Labridae, Siganidae and Chaetodontidae) did not differ significantly between reserve and fished zones at either island group. This is the most convincing data to date that the management zoning of the world's largest marine park has been effective, at least for coral trout on inshore reefs.

A unique assemblage of tropical and temperate marine organisms characterizes the Houtman Abrolhos Islands, four clusters of islands and reefs off the coast of mid-Western Australia. Four reef observation areas or marine protected areas (MPAs) were established in 1994 to examine their value in protecting vulnerable reef fish species, including the sub-tropical wrasse, Choerodon rubescens, and the coral trout, Plectropomus leopardus. In 1993 and 1994 (prior to protection), population densities and body sizes were monitored at two island groups (Easter and Wallabi). At each location, the MPAs and the equivalent ‘control’ areas to remain open to fishing were monitored by underwater visual censuses. These closed and open areas were subsequently monitored four more times between 1995 and 2002 to assess long-term trends in abundance and population structure. Populations of the wrasse, C. rubescens, did not appear to respond to protection, exhibiting irregular fluctuations in both closed and open areas throughout the study. In contrast, although there were no significant increases for P. leopardus for the first three years of closure, after eight years of protection there were significantly larger numbers of P. leopardus in the closed areas. There was a three-fold increase at the Easter Group and a seven-fold increase at the Wallabi Group, relative to open fishing areas, attributed primarily to reduced fishing mortality. Significant closed areas (17% of the P. leopardus habitat) provided substantial stock-wide impacts. The data also indicate that the MPAs can be effective where some forms of fishing (such as lobster fishing) are permitted which are compatible with the objectives of the MPA. While MPAs are clearly an effective tool for increasing the local abundance of some reef fishes, the spatial and temporal scales required for their success may vary among species.