Two Hundred Years of Local Avian Extinctions in Eastern Amazonia

Local, regional, and global extinctions caused by habitat loss, degradation, and fragmentation have been widely reported for the tropics. The patterns and drivers of this loss of species are now increasingly well known in Amazonia, but there remains a significant gap in understanding of long‐term trends in species persistence and extinction in anthropogenic landscapes. Such a historical perspective is critical for understanding the status and trends of extant biodiversity as well as for identifying priorities to halt further losses. Using extensive historical data sets of specimen records and results of contemporary surveys, we searched for evidence of local extinctions of a terra firma rainforest avifauna over 200 years in a 2500 km² eastern Amazonian region around the Brazilian city of Belém. This region has the longest history of ornithological fieldwork in the entire Amazon basin and lies in the highly threatened Belém Centre of Endemism. We also compared our historically inferred extinction events with extensive data on species occurrences in a sample of catchments in a nearby municipality (Paragominas) that encompass a gradient of past forest loss. We found evidence for the possible extinction of 47 species (14% of the regional species pool) that were unreported from 1980 to 2013 (80% last recorded between 1900 and 1980). Seventeen species appear on the International Union for Conservation of Nature Red List, and many of these are large‐bodied. The species lost from the region immediately around Belém are similar to those which are currently restricted to well‐forested catchments in Paragominas. Although we anticipate the future rediscovery or recolonization of some species inferred to be extinct by our calculations, we also expect that there are likely to be additional local extinctions, not reported here, given the ongoing loss and degradation of remaining areas of native vegetation across eastern Amazonia. Doscientos Años de Extinciones Locales de Aves en la Amazonia Oriental     

Combined Effects of Levels of Protection and Environmental Variables at Different Spatial Resolutions on Fish Assemblages in a Marine Protected Area

Abstract: The links between species–environment relations and species’ responses to protection are unclear, but the objectives of marine protected areas (MPAs) are most likely to be achieved when those relations are known and inform MPA design. The components of a species’ habitat vary with the spatial resolution of the area considered. We characterized areas at two resolutions: 250 m² (transect) and approximately 30,000 m² (seascape). We considered three categories of environmental variables: substrate type, bottom complexity, and depth. We sought to determine at which resolution habitat characteristics were a better predictor of abundance and species composition of fishes and whether the relations with environmental variables at either resolution affected species’ responses to protection. Habitat features accounted for a larger proportion of spatial variation in species composition and abundances than differences in protection status. This spatial variation was explained best by habitat characteristics at the seascape level than at the transect level. Species’ responses to protected areas were specific to particular seascape characteristics, primarily depth, and bottom complexity. Our method may be useful for prioritizing marine areas for protection, designing MPAs, and monitoring their effectiveness. It identified areas that provided natural shelter, areas acting as buffer zones, and areas where fish species were most responsive to protection. The identification of such areas is necessary for cost‐effective establishment and monitoring of MPAs.     

Experimental Test of Postfire Management in Pine Forests: Impact of Salvage Logging versus Partial Cutting and Nonintervention on Bird–Species Assemblages

Abstract: There is an intense debate about the effects of postfire salvage logging versus nonintervention policies on regeneration of forest communities, but scant information from experimental studies is available. We manipulated a burned forest area on a Mediterranean mountain to experimentally analyze the effect of salvage logging on bird–species abundance, diversity, and assemblage composition. We used a randomized block design with three plots of approximately 25 ha each, established along an elevational gradient in a recently burned area in Sierra Nevada Natural and National Park (southeastern Spain). Three replicates of three treatments differing in postfire burned wood management were established per plot: salvage logging, nonintervention, and an intermediate degree of intervention (felling and lopping most of the trees but leaving all the biomass). Starting 1 year after the fire, we used point sampling to monitor bird abundance in each treatment for 2 consecutive years during the breeding and winter seasons (720 censuses total). Postfire burned‐wood management altered species assemblages. Salvage logged areas had species typical of open‐ and early‐successional habitats. Bird species that inhabit forests were still present in the unsalvaged treatments even though trees were burned, but were almost absent in salvage‐logged areas. Indeed, the main dispersers of mid‐ and late‐successional shrubs and trees, such as thrushes (Turdus spp.) and the European Jay (Garrulus glandarius) were almost restricted to unsalvaged treatments. Salvage logging might thus hamper the natural regeneration of the forest through its impact on assemblages of bird species. Moreover, salvage logging reduced species abundance by 50% and richness by 40%, approximately. The highest diversity at the landscape level (gamma diversity) resulted from a combination of all treatments. Salvage logging may be positive for bird conservation if combined in a mosaic with other, less‐aggressive postfire management, but stand‐wide management with harvest operations has undesirable conservation effects.     

Possible Extinction Vortex for a Population of Iberian Lynx on the Verge of Extirpation

Abstract: Theory suggests that demographic and genetic traits deteriorate (i.e., fitness and genetic diversity decrease) when populations become small, and that such deterioration could precipitate positive feedback loops called extinction vortices. We examined whether demographic attributes and genetic traits have changed over time in one of the 2 remaining small populations of the highly endangered Iberian lynx (Lynx pardinus) in Doñana, Spain. From 1983 to 2008, we recorded nontraumatic mortality rates, litter size, offspring survival, age at territory acquisition, and sex ratio. We combined these demographic attributes with measures of inbreeding and genetic diversity at neutral loci (microsatellites) and genes subjected to selection (major histocompatibility complex). Data on demographic traits were obtained through capture and radio tracking, checking dens during breeding, track surveys, and camera trapping. For genetic analyses, we obtained blood or tissue samples from captured or necropsied individuals or from museum specimens. Over time a female‐biased sex ratio developed, age of territory acquisition decreased, mean litter size decreased, and rates of nontraumatic mortality increased, but there were no significant changes in overall mortality rates, standardized individual heterozygosity declined steadily, and allelic diversity of exon 2 of class II major histocompatibility complex DRB genes remained constant (2 allelic variants present in all individuals analyzed). Changes in sex ratio and age of territory acquisition may have resulted from demographic stochasticity, whereas changes in litter size and nontraumatic mortality may be related to observed increases in inbreeding. Concomitant deterioration of both demographic attributes and genetic traits is consistent with an extinction vortex. The co‐occurrence, with or without interaction, of demographic and genetic deterioration may explain the lack of success of conservation efforts with the Doñana population of Iberian lynx.     

Heterozygosity‐Fitness Correlations and Inbreeding Depression in Two Critically Endangered Mammals

The relation among inbreeding, heterozygosity, and fitness has been studied primarily among outbred populations, and little is known about these phenomena in endangered populations. Most researchers conclude that the relation between coefficient of inbreeding estimated from pedigrees and fitness traits (inbreeding‐fitness correlations) better reflects inbreeding depression than the relation between marker heterozygosity and fitness traits (heterozygosity‐fitness correlations). However, it has been suggested recently that heterozygosity‐fitness correlations should only be expected when inbreeding generates extensive identity disequilibrium (correlations in heterozygosity and homozygosity across loci throughout the genome). We tested this hypothesis in Mohor gazelle (Gazella dama mhorr) and Iberian lynx (Lynx pardinus). For Mohor gazelle, we calculated the inbreeding coefficient and measured heterozygosity at 17 microsatellite loci. For Iberian lynx, we measured heterozygosity at 36 microsatellite loci. In both species we estimated semen quality, a phenotypic trait directly related to fitness that is controlled by many loci and is affected by inbreeding depression. Both species showed evidence of extensive identity disequilibrium, and in both species heterozygosity was associated with semen quality. In the Iberian lynx the low proportion of normal sperm associated with low levels of heterozygosity was so extreme that it is likely to limit the fertility of males. In Mohor gazelle, although heterozygosity was associated with semen quality, inbreeding coefficient was not. This result suggests that when coefficient of inbreeding is calculated on the basis of a genealogy that begins after a long history of inbreeding, the coefficient of inbreeding fails to capture previous demographic information because it is a poor estimator of accumulated individual inbreeding. We conclude that among highly endangered species with extensive identity disequilibrium, examination of heterozygosity‐fitness correlations may be an effective way to detect inbreeding depression, whereas inbreeding‐fitness correlations may be poor indicators of inbreeding depression if the pedigree does not accurately reflect the history of inbreeding. Correlaciones Heterocigosidad‐ Adaptabilidad y Depresión Endogámica en Dos Especies de Mamíferos Críticamente en Peligro     

Effects of Forest Fragmentation on Seed Dispersal and Seedling Establishment in Ornithochorous Trees

Abstract: Habitat fragmentation increases seed dispersal limitation across the landscape and may also affect subsequent demographic stages such as seedling establishment. Thus, the development of adequate plans for forest restoration requires an understanding of mechanisms by which fragmentation hampers seed delivery to deforested areas and knowledge of how fragmentation affects the relationship between seed‐deposition patterns and seedling establishment. We evaluated the dispersal and recruitment of two bird‐dispersed, fleshy‐fruited tree species (Crataegus monogyna and Ilex aquifolium) in fragmented secondary forests of northern Spain. Forest fragmentation reduced the probability of seed deposition for both trees because of decreased availability of woody perches and fruit‐rich neighborhoods for seed dispersers, rather than because of reductions in tree cover by itself. The effects of fragmentation went beyond effects on the dispersal stage in Crataegus because seedling establishment was proportional to the quantities of bird‐dispersed seeds arriving at microsites. In contrast, postdispersal mortality in Ilex was so high that it obscured the seed‐to‐seedling transition. These results suggest that the effects of fragmentation are not necessarily consistent across stages of recruitment across species. Habitat management seeking to overcome barriers to forest recovery must include the preservation, and even the planting, of fleshy‐fruited trees in the unforested matrix as a measure to encourage frugivorous birds to enter into open and degraded areas. An integrative management strategy should also explicitly consider seed‐survival expectancies at microhabitats to preserve plant‐population dynamics and community structure in fragmented landscapes.     

Biodiversity Loss in Latin American Coffee Landscapes: Review of the Evidence on Ants,Birds, and Trees

Abstract: Studies have documented biodiversity losses due to intensification of coffee management (reduction in canopy richness and complexity). Nevertheless, questions remain regarding relative sensitivity of different taxa, habitat specialists, and functional groups, and whether implications for biodiversity conservation vary across regions. We quantitatively reviewed data from ant, bird, and tree biodiversity studies in coffee agroecosystems to address the following questions: Does species richness decline with intensification or with individual vegetation characteristics? Are there significant losses of species richness in coffee‐management systems compared with forests? Is species loss greater for forest species or for particular functional groups? and Are ants or birds more strongly affected by intensification? Across studies, ant and bird richness declined with management intensification and with changes in vegetation. Species richness of all ants and birds and of forest ant and bird species was lower in most coffee agroecosystems than in forests, but rustic coffee (grown under native forest canopies) had equal or greater ant and bird richness than nearby forests. Sun coffee (grown without canopy trees) sustained the highest species losses, and species loss of forest ant, bird, and tree species increased with management intensity. Losses of ant and bird species were similar, although losses of forest ants were more drastic in rustic coffee. Richness of migratory birds and of birds that forage across vegetation strata was less affected by intensification than richness of resident, canopy, and understory bird species. Rustic farms protected more species than other coffee systems, and loss of species depended greatly on habitat specialization and functional traits. We recommend that forest be protected, rustic coffee be promoted, and intensive coffee farms be restored by augmenting native tree density and richness and allowing growth of epiphytes. We also recommend that future research focus on potential trade‐offs between biodiversity conservation and farmer livelihoods stemming from coffee production.     

Minimizing the Cost of Keeping Options Open for Conservation in a Changing Climate

Policy documents advocate that managers should keep their options open while planning to protect coastal ecosystems from climate‐change impacts. However, the actual costs and benefits of maintaining flexibility remain largely unexplored, and alternative approaches for decision making under uncertainty may lead to better joint outcomes for conservation and other societal goals. For example, keeping options open for coastal ecosystems incurs opportunity costs for developers. We devised a decision framework that integrates these costs and benefits with probabilistic forecasts for the extent of sea‐level rise to find a balance between coastal ecosystem protection and moderate coastal development. Here, we suggest that instead of keeping their options open managers should incorporate uncertain sea‐level rise predictions into a decision‐making framework that evaluates the benefits and costs of conservation and development. In our example, based on plausible scenarios for sea‐level rise and assuming a risk‐neutral decision maker, we found that substantial development could be accommodated with negligible loss of environmental assets. Characterization of the Pareto efficiency of conservation and development outcomes provides valuable insight into the intensity of trade‐offs between development and conservation. However, additional work is required to improve understanding of the consequences of alternative spatial plans and the value judgments and risk preferences of decision makers and stakeholders. Minimizando el Costo de Mantener Opciones Abiertas para la Conservación en un Clima Cambiante