Global patterns and drivers of avian extinctions at the species and subspecies level

Birds have long fascinated scientists and travellers, so their distribution and abundance through time have been better documented than those of other organisms. Many bird species are known to have gone extinct, but information on subspecies extinctions has never been synthesised comprehensively. We reviewed the timing, spatial patterns, trends and causes of avian extinctions on a global scale, identifying 279 ultrataxa (141 monotypic species and 138 subspecies of polytypic species) that have gone extinct since 1500. Species extinctions peaked in the early 20th century, then fell until the mid 20th century, and have subsequently accelerated. However, extinctions of ultrataxa peaked in the second half of the 20th century. This trend reflects a consistent decline in the rate of extinctions on islands since the beginning of the 20th century, but an acceleration in the extinction rate on continents. Most losses (78.7% of species and 63.0% of subspecies) occurred on oceanic islands. Geographic foci of extinctions include the Hawaiian Islands (36 taxa), mainland Australia and islands (29 taxa), the Mascarene Islands (27 taxa), New Zealand (22 taxa) and French Polynesia (19 taxa). The major proximate drivers of extinction for both species and subspecies are invasive alien species (58.2% and 50.7% of species and subspecies, respectively), hunting (52.4% and 18.8%) and agriculture, including non-timber crops and livestock farming (14.9% and 31.9%). In general, the distribution and drivers of subspecific extinctions are similar to those for species extinctions. However, our finding that, when subspecies are considered, the extinction rate has accelerated in recent decades is both novel and alarming

Regional avian species declines estimated from volunteer-collected long-term data using List Length Analysis

Long-term systematic population monitoring data sets are rare but are essential in identifying changes in species abundance. In contrast, community groups and natural history organizations have collected many species lists. These represent a large, untapped source of information on changes in abundance but are generally considered of little value. The major problem with using species lists to detect population changes is that the amount of effort used to obtain the list is often uncontrolled and usually unknown. It has been suggested that using the number of species on the list, the "list length,'' can be a measure of effort. This paper significantly extends the utility of Franklin's approach using Bayesian logistic regression. We demonstrate the value of List Length Analysis to model changes in species prevalence (i.e., the proportion of lists on which the species occurs) using bird lists collected by a local bird club over 40 years around Brisbane, southeast Queensland, Australia. We estimate the magnitude and certainty of change for 269 bird species and calculate the probabilities that there have been declines and increases of given magnitudes

Adapting global biodiversity indicators to the national scale: A Red List Index for Australian birds

The Red List Index (RLI), which uses information from the IUCN Red List to track trends in the projected overall extinction risk of sets of species, is among the indicators adopted by the world’s governments to assess performance under the Convention on Biological Diversity and the United Nations Millennium Development Goals. For greatest impact, such indicators need to be measured and used at a national scale as well as globally. We present the first application of the RLI based on assessments of extinction risk at the national scale using IUCN’s recommended methods, evaluating trends in the status of Australian birds for 1990–2010. We calculated RLIs based on the number of taxa in each Red List category and the number that changed categories between assessments in 1990, 2000 and 2010 as a result of genuine improvement or deterioration in status. A novel comparison between trends at the species and ultrataxon (subspecies or monotypic species) level showed that these were remarkably similar, suggesting that current global RLI trends at the species level may also be a useful surrogate for tracking losses in genetic diversity at this scale, for which no global measures currently exist. The RLI for Australia is declining faster than global rates when migratory shorebirds and seabirds are included, but not when changes resulting from threats in Australia alone are considered. The RLI of oceanic island taxa has declined faster than those on the continent or on continental islands. There were also differences in the performance of different jurisdictions within Australia

Evaluating protected area effectiveness using bird lists in the Australian Wet Tropics

AimProtected areas underpin many global conservation efforts. However, it is often unclear whether they are effective in maintaining their biodiversity values, both absolutely, and also relative to other conservation actions or land uses. Longitudinal population data are critical for determining protected area performance robustly, but such data are rare. As such, there is often insufficient information with which to make adequate, informed decisions for policy and management. Conversely, informally collected data, such as species lists, are common, especially for birds, and they are often the only source of historical data. The aim of this study was to use list data to evaluate the contribution of protected areas to the conservation of endemic birds

Predicting avian distributions to evaluate spatiotemporal overlap with locust control operations in eastern Australia

Locusts and grasshoppers cause considerable economic damage to agriculture worldwide. The Australian Plague Locust Commission uses multiple pesticides to control locusts in eastern Australia. Avian exposure to agricultural pesticides is of conservation concern, especially in the case of rare and threatened species. The aim of this study was to evaluate the probability of pesticide exposure of native avian species during operational locust control based on knowledge of species occurrence in areas and times of application. Using presence-absence data provided by the Birds Australia Atlas for 1998 to 2002, we developed a series of generalized linear models to predict avian occurrences on a monthly basis in 0.5 degrees grid cells for 280 species over 2 million km 2 in eastern Australia. We constructed species-specific models relating occupancy patterns to survey date and location, rainfall, and derived habitat preference. Model complexity depended on the number of observations available. Model output was the probability of occurrence for each species at times and locations of past locust control operations within the 5-year study period. Given the high spatiotemporal variability of locust control events, the variability in predicted bird species presence was high, with 108 of the total 280 species being included at least once in the top 20 predicted species for individual space-time events. The models were evaluated using field surveys collected between 2000 and 2005, at sites with and without locust outbreaks. Model strength varied among species. Some species were under- or over-predicted as times and locations of interest typically did not correspond to those in the prediction data set and certain species were likely attracted to locusts as a food source. Field surveys demonstrated the utility of the spatially explicit species lists derived from the models but also identified the presence of a number of previously unanticipated species. These results also emphasize the need for special consideration of rare and threatened species that are poorly predicted by presence-absence models. This modeling exercise was a useful a priori approach in species risk assessments to identify species present at times and locations of locust control applications, and to discover gaps in our knowledge and need for further focused data collection Copyright 2009 by the Ecological Society ot America

Loss of Cultural and Functional Diversity Associated With Birds Across the Urbanization Gradient in a Tropical City

Birds provide many ecosystem services to people, including provisioning, regulating and cultural services. People attribute multiple cultural values to ecosystems and biodiversity and the diversity of these cultural values can be considered as cultural diversity. While human-nature interactions occur more frequently in cities and urbanization negatively affects different facets of avian biodiversity, little is known about its consequence for cultural diversity. Here, we assess how the urbanization gradient in Campo Grande, a Brazilian city in the Cerrado biodiversity hotspot, affects functional and cultural diversity associated with birds and if functional and cultural diversity are congruent. We also investigate the relation between urbanization gradient with functional traits and cultural values, weighted by species abundance. We used a dataset based on bird surveyed in 61 landscapes along a gradient of impervious surface cover. To estimate functional and cultural diversity, we used indices that estimate richness and divergence of functional traits and cultural values. We found that urbanization affected functional and cultural richness negatively, while there was no effect on functional and cultural divergence. Functional and cultural richness and functional and cultural divergence were weakly, but significantly correlated. Bird species that nest on trees decreased and those that nest in artificial structures and on the ground increased along the impervious surface gradient. Body size, diet, habitat, mating system, flock behavior, and all cultural values (number of times the species was mentioned by football teams, music or poetry, city flags and anthems, and folklore tales) were not significantly affected by impervious surface. The negative relationship between impervious surface and bird cultural richness may indicate that people living in more urbanized areas experience nature less compared to people in less urbanized areas, which can affect their psychological well-being. In these highly urbanized areas, contact with culturally valued birds and cultural services provided by birds may also diminish. The negative relationship between functional richness and urbanization also indicate that highly urbanized areas may be losing important ecosystems services provided by birds

The State of Migratory Landbirds in the East Asian Flyway: Distributions, Threats, and Conservation Needs

With nearly 400 migratory landbird species, the East Asian Flyway is the most diverse of the world’s flyways. This diversity is a consequence of the varied ecological niches provided by biomes ranging from broadleaf forests to arctic tundra and accentuated by complex biogeographic processes. The distribution and migration ecology of East Asian landbirds is still inadequately known, but a recent explosion in the number of studies tracking the migration of raptors, cuckoos, kingfishers and passerines has greatly increased our knowledge about the stopover and wintering ecology of many species, and the migratory routes that link northeast Eurasia and the Asian tropics. Yet the East Asian Flyway also supports the highest number of threatened species among flyways. Strong declines have been detected in buntings (Emberizidae) and other long-distance migrants. While the conservation of migratory landbirds in this region has largely focused on unsustainable hunting, there are other threats, such as habitat loss and increased agro-chemical use driven directly by land cover change and climate-related processes. Important knowledge gaps to be addressed include (1) threats affecting species in different parts of their annual cycle, (2) range-wide population trends, (3) ecological requirements and habitat use during the non-breeding season, and (4) the conservation status of critical wintering sites (including understudied farming landscapes, such as rice fields) and migration bottlenecks along the flyway

An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers

Introduction: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers. Methods: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals. Results: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk. Conclusions: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.Peer reviewe

IFNγ and IL-12 restrict Th2 responses during Helminth/Plasmodium co-infection and promote IFNγ from Th2 cells

Parasitic helminths establish chronic infections in mammalian hosts. Helminth/Plasmodium co-infections occur frequently in endemic areas. However, it is unclear whether Plasmodium infections compromise anti-helminth immunity, contributing to the chronicity of infection. Immunity to Plasmodium or helminths requires divergent CD4+ T cell-driven responses, dominated by IFNγ or IL-4, respectively. Recent literature has indicated that Th cells, including Th2 cells, have phenotypic plasticity with the ability to produce non-lineage associated cytokines. Whether such plasticity occurs during co-infection is unclear. In this study, we observed reduced anti-helminth Th2 cell responses and compromised anti-helminth immunity during Heligmosomoides polygyrus and Plasmodium chabaudi co-infection. Using newly established triple cytokine reporter mice (Il4gfpIfngyfpIl17aFP635), we demonstrated that Il4gfp+ Th2 cells purified from in vitro cultures or isolated ex vivo from helminth-infected mice up-regulated IFNγ following adoptive transfer into Rag1-/- mice infected with P. chabaudi. Functionally, Th2 cells that up-regulated IFNγ were transcriptionally re-wired and protected recipient mice from high parasitemia. Mechanistically, TCR stimulation and responsiveness to IL-12 and IFNγ, but not type I IFN, was required for optimal IFNγ production by Th2 cells. Finally, blockade of IL-12 and IFNγ during co-infection partially preserved anti-helminth Th2 responses. In summary, this study demonstrates that Th2 cells retain substantial plasticity with the ability to produce IFNγ during Plasmodium infection. Consequently, co-infection with Plasmodium spp. may contribute to the chronicity of helminth infection by reducing anti-helminth Th2 cells and converting them into IFNγ-secreting cells

Post-intervention Status in Patients With Refractory Myasthenia Gravis Treated With Eculizumab During REGAIN and Its Open-Label Extension

OBJECTIVE: To evaluate whether eculizumab helps patients with anti-acetylcholine receptor-positive (AChR+) refractory generalized myasthenia gravis (gMG) achieve the Myasthenia Gravis Foundation of America (MGFA) post-intervention status of minimal manifestations (MM), we assessed patients' status throughout REGAIN (Safety and Efficacy of Eculizumab in AChR+ Refractory Generalized Myasthenia Gravis) and its open-label extension. METHODS: Patients who completed the REGAIN randomized controlled trial and continued into the open-label extension were included in this tertiary endpoint analysis. Patients were assessed for the MGFA post-intervention status of improved, unchanged, worse, MM, and pharmacologic remission at defined time points during REGAIN and through week 130 of the open-label study. RESULTS: A total of 117 patients completed REGAIN and continued into the open-label study (eculizumab/eculizumab: 56; placebo/eculizumab: 61). At week 26 of REGAIN, more eculizumab-treated patients than placebo-treated patients achieved a status of improved (60.7% vs 41.7%) or MM (25.0% vs 13.3%; common OR: 2.3; 95% CI: 1.1-4.5). After 130 weeks of eculizumab treatment, 88.0% of patients achieved improved status and 57.3% of patients achieved MM status. The safety profile of eculizumab was consistent with its known profile and no new safety signals were detected. CONCLUSION: Eculizumab led to rapid and sustained achievement of MM in patients with AChR+ refractory gMG. These findings support the use of eculizumab in this previously difficult-to-treat patient population. CLINICALTRIALSGOV IDENTIFIER: REGAIN, NCT01997229; REGAIN open-label extension, NCT02301624. CLASSIFICATION OF EVIDENCE: This study provides Class II evidence that, after 26 weeks of eculizumab treatment, 25.0% of adults with AChR+ refractory gMG achieved MM, compared with 13.3% who received placebo