Surveys at Bagan Percut, Sumatra, reveal its international importance to migratory shorebirds and breeding herons

The Bagan Percut region of north-eastern Sumatra, Indonesia, is becoming well known for its large concentrations of migratory shorebirds. From January to June 2011 we made monthly counts of shorebirds and waterbirds at four mudflats and one heron rookery. Fifty-one species were recorded, including 35 migratory species, and eight breeding species in the rookery. We counted 20,114 migratory shorebirds (mudflats) and 45,648 breeding waterbirds (rookery) over six months of surveys. We observed >1% of the East Asian-Australasian flyway population of five species of migratory shorebirds: Nordmann’s Greenshank Tringa guttifer (globally Endangered), Lesser Sand Plover Charadrius mongolus, Pacific Golden Plover Pluvialis fulva, Eurasian Curlew Numenius arquata, and Ruddy Turnstone Arenaria interpres. Our results support the work of others that indicate that Bagan Percut is an important habitat for wintering, migrating, and summering shorebirds. We recommend that Bagan Percut be added to the East Asian-Australasian Flyway Partnership list of internationally important wetlands because the area meets all three criteria for inclusion

A New Species of Muscicapa Flycatcher from Sulawesi, Indonesia

The Indonesian island of Sulawesi, a globally important hotspot of avian endemism, has been relatively poorly studied ornithologically, to the extent that several new bird species from the region have been described to science only recently, and others have been observed and photographed, but never before collected or named to science. One of these is a new species of Muscicapa flycatcher that has been observed on several occasions since 1997. We collected two specimens in Central Sulawesi in 2012, and based on a combination of morphological, vocal and genetic characters, we describe the new species herein, more than 15 years after the first observations. The new species is superficially similar to the highly migratory, boreal-breeding Gray-streaked Flycatcher Muscicapa griseisticta, which winters in Sulawesi; however, the new species differs strongly from M. griseisticta in several morphological characters, song, and mtDNA. Based on mtDNA, the new species is only distantly related to M. griseisticta, instead being a member of the M. dauurica clade. The new species is evidently widely distributed in lowland and submontane forest throughout Sulawesi. This wide distribution coupled with the species' apparent tolerance of disturbed habitats suggests it is not currently threatened with extinction.This project was funded by the National Geographic Society (NGS CRE 8919-11; granted to PCR), the Loke Wan Tho Memorial Foundation (granted to DLY), and an EIPR scholarship at the University of Adelaide (granted to JBCH). Labwork for this project was co-funded by a National University of Singapore Faculty of Science start-up grant to FER (WBS R-154-000-570-133). We thank RISTEK for issuing the national research permits (for 2011, 0215/SIP/FRP/VI/2011; for 2012, 183/SIP/FRP/SM/VI/2012) and Lore Lindu National Park for permit letters. The Research Centre for Biology-LIPI supported DMP and DDP in their field research and provided facilities for laboratory analysis. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The World's Rediscovered Species: Back from the Brink?

Each year, numerous species thought to have disappeared are rediscovered. Yet, do these rediscoveries represent the return of viable populations or the delayed extinction of doomed species? We document the number, distribution and conservation status of rediscovered amphibian, bird, and mammal species globally. Over the past 122 years, at least 351 species have been rediscovered, most occurring in the tropics. These species, on average, were missing for 61 years before being rediscovered (range of 3–331 years). The number of rediscoveries per year increased over time and the majority of these rediscoveries represent first documentations since their original description. Most rediscovered species have restricted ranges and small populations, and 92% of amphibians, 86% of birds, and 86% of mammals are highly threatened, independent of how long they were missing or when they were rediscovered. Under the current trends of widespread habitat loss, particularly in the tropics, most rediscovered species remain on the brink of extinction

Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15–20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases. Methods: We report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded. Results: No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5–528.7, P = 1.1 × 10−4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3–8.2], P = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], P = 3.4 × 10−3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3–8.4], P = 7.7 × 10−8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10−5). Conclusions: Rare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old

Land Cover Sampling Biases Associated with Roadside Bird Surveys

Roadside surveys such as the Breeding Bird Survey (BBS) are widely used to assess the relative abundance of bird populations. The accuracy of roadside surveys depends on the extent to which surveys from roads represent the entire region under study. We quantified roadside land cover sampling bias in Tennessee, USA, by comparing land cover proportions near roads to proportions of the surrounding region. Roadside surveys gave a biased estimate of patterns across the region because some land cover types were over- or underrepresented near roads. These biases changed over time, introducing varying levels of distortion into the data. We constructed simulated population trends for five bird species of management interest based on these measured roadside sampling biases and on field data on bird abundance. These simulations indicated that roadside surveys may give overly negative assessments of the population trends of early successional birds and of synanthropic birds, but not of late-successional birds. Because roadside surveys are the primary source of avian population trend information in North America, we conclude that these surveys should be corrected for roadside land cover sampling bias. In addition, current recommendations about the need to create more early successional habitat for birds may need reassessment in the light of the undersampling of this habitat by roads

Simulated birdwatchers' playback affects the behavior of two tropical birds.

Although recreational birdwatchers may benefit conservation by generating interest in birds, they may also have negative effects. One such potentially negative impact is the widespread use of recorded vocalizations, or "playback," to attract birds of interest, including range-restricted and threatened species. Although playback has been widely used to test hypotheses about the evolution of behavior, no peer-reviewed study has examined the impacts of playback in a birdwatching context on avian behavior. We studied the effects of simulated birdwatchers' playback on the vocal behavior of Plain-tailed Wrens Thryothorus euophrys and Rufous Antpittas Grallaria rufula in Ecuador. Study species' vocal behavior was monitored for an hour after playing either a single bout of five minutes of song or a control treatment of background noise. We also studied the effects of daily five minute playback on five groups of wrens over 20 days. In single bout experiments, antpittas made more vocalizations of all types, except for trills, after playback compared to controls. Wrens sang more duets after playback, but did not produce more contact calls. In repeated playback experiments, wren responses were strong at first, but hardly detectable by day 12. During the study, one study group built a nest, apparently unperturbed, near a playback site. The playback-induced habituation and changes in vocal behavior we observed suggest that scientists should consider birdwatching activity when selecting research sites so that results are not biased by birdwatchers' playback. Increased vocalizations after playback could be interpreted as a negative effect of playback if birds expend energy, become stressed, or divert time from other activities. In contrast, the habituation we documented suggests that frequent, regular birdwatchers' playback may have minor effects on wren behavior

Avian Habitat Preference in Tropical Forest Restoration in Southern Costa Rica

An important question for tropical forest restoration is whether degraded lands can be actively managed to attract birds. We censused birds and measured vegetation structure at 27 stations in young (6–9‐yr old) actively and passively restored pasture and old growth forest at Las Cruces Biological Station in southern Costa Rica. During 481 10‐min point counts, we detected a high diversity—186 species— of birds using the restoration area. Surprisingly, species richness and detection frequency did not differ among habitats, and proportional similarity of bird assemblages to old growth forest did not differ between restoration treatments. Bird detection frequency was instead explained by exotic grass cover and understory stem density—vegetation structures that were not strongly impacted by active restoration. The similarity of bird assemblages in actively and passively restored forest may be attributed to differential habitat preferences within and among feeding guilds, low structural contrast between treatments, or the effect of nucleation from actively restored plots into passively restored areas. Rapid recovery of vegetation in this recently restored site is likely due to its proximity to old growth forest and the lack of barriers to effective seed dispersal. Previous restoration studies in highly binary environments (i.e., open pasture vs. tree plantation) have found strong differences in bird abundance and richness. Our data contradict this trend, and suggest that tropical restoration ecologists should carefully consider: (1) when the benefits of active restoration outweigh the cost of implementation; and (2) which avian guilds should be used to measure restoration success given differential responses to habitat structure.J. Leighton Reid, J. Berton C. Harris and Rakan A. Zahaw

Description of the nest and parental care of the Chestnut-Naped Antpitta (Grallaria nuchalis) from southern Ecuador

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Distribution, plumage, and conservation status of the endemic esmeraldas woodstar (Chaetocercus berlepschi) of western Ecuador

The Esmeraldas Woodstar (Chaetocercus berlepschi) is a poorly known and endangered hummingbird endemic to lowland and foothill moist forest in coastal western Ecuador. We encountered 11 new localities, observed two copulations, and found 26 nests of the species from October 2007 to April 2008. We observed the generally accepted descriptions of the female must have come from mis-labeled specimens of juvenile males and were incorrect. We collected the first three confirmed females of the species and describe their characteristics. The correct identification of female C. berlepschi and recognition of the species' breeding habitat should facilitate more effective conservation of the species.J. Berton C. Harris, Ana E. Ágreda, Mery E. Juiña and Bernd P. Freymannhttp://www.bioone.org/toc/wils/121/