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The avifauna of Indonesia is one of the richest in the world but the taxonomic status of many species remains poorly documented. The sole species of scops owl known from Lombok has long been assigned to the widespread Moluccan Scops Owl Otus magicus on the basis of superficial similarities in morphology. Field work in 2003 has shown that the territorial song of the scops owls inhabiting the foothills of Gunung Rinjani differs dramatically from that of O. magicus and is more similar to those of Rufescent Scops Owl O. rufescens and Singapore Scops Owl O. cnephaeus. Detailed comparisons of sound recordings and museum specimens with those of other scops owls in Wallacea and the Indo-Malayan region have confirmed the distinctiveness of the Lombok population. We describe Otus jolandae as a new species, the Rinjani Scops Owl. It is locally common at elevations from 25-1350 m. and occurs within Gunung Rinjani National Park. The new species is known from seven specimens collected by Alfred Everett in 1896. Otus jolandae represents the first endemic bird species from Lombok.

Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches. Recent discussion focuses on the best method for delineating microbial taxa, based on either exact sequence variants (ESVs) or traditional operational taxonomic units (OTUs) of marker gene sequences. We sought to test if the binning approach (ESVs versus 97% OTUs) affected the ecological conclusions of a large field study. The data set included sequences targeting all bacteria (16S rRNA) and fungi (internal transcribed spacer [ITS]), across multiple environments diverging markedly in abiotic conditions, over three collection times. Despite quantitative differences in microbial richness, we found that all α and β diversity metrics were highly positively correlated ( r > 0.90) between samples analyzed with both approaches. Moreover, the community composition of the dominant taxa did not vary between approaches. Consequently, statistical inferences were nearly indistinguishable. Furthermore, ESVs only moderately increased the genetic resolution of fungal and bacterial diversity (1.3 and 2.1 times OTU richness, respectively). We conclude that for broadscale (e.g., all bacteria or all fungi) α and β diversity analyses, ESV or OTU methods will often reveal similar ecological results. Thus, while there are good reasons to employ ESVs, we need not question the validity of results based on OTUs. IMPORTANCE Microbial ecologists have made exceptional improvements in our understanding of microbiomes in the last decade due to breakthroughs in sequencing technologies. These advances have wide-ranging implications for fields ranging from agriculture to human health. Due to limitations in databases, the majority of microbial ecology studies use a binning approach to approximate taxonomy based on DNA sequence similarity. There remains extensive debate on the best way to bin and approximate this taxonomy. Here we examine two popular approaches using a large field-based data set examining both bacteria and fungi and conclude that there are not major differences in the ecological outcomes. Thus, it appears that standard microbial community analyses are not overly sensitive to the particulars of binning approaches.

The niche divergence hypothesis proposes that the evolution and maintenance of colour polymorphism is based on a mechanism of disruptive selection. In a trophic context, the hypothesis predicts that individuals differing in colour vary in their trophic niche, either because they differ in foraging efficiency or feed in different habitats. A major evolutionary conundrum is how these expectations are affected by variation in trophic quality. Using an owl species with colour plumage polymorphism, the Eurasian scops owl Otus scops, we examined diet and habitat segregation during reproduction in relation to plumage colouration and trophic quality. Intensive sampling revealed that trophic quality for scops owls (i.e. abundance of grasshoppers and locusts) varied more among territories than between years, but scops owls did not segregate among territories of different quality by their colouration. However, we found that sex, plumage colouration and territory differences in trophic quality explained differences in the degree of dietary specialization. Brownish males delivered a higher diversity of prey to the nest than greyish ones in high trophic quality territories. We also found that the more diverse the diet provided by males, the heavier the owlets at fledging. Our study provides evidence for a different sensitivity to trophic quality of the colour morphs with potential fitness consequences in scops owls. We highlight the importance of studying the mechanisms leading to the persistence of colour polymorphism in patchy environments, since segregation may pass otherwise unnoticed if only habitats or years with similar conditions are considered.

We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome- c -oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico , in vitro , and in situ . We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.

Soil-borne plant diseases are increasingly causing devastating losses in agricultural production. The development of a more refined model for disease prediction can aid in reducing crop losses through the use of preventative control measures or soil fallowing for a planting season. The emergence of high-throughput DNA sequencing technology has provided unprecedented insight into the microbial composition of diseased versus healthy soils. However, a single independent case study rarely yields a general conclusion predictive of the disease in a particular soil. Here, we attempt to account for the differences among various studies and plant varieties using a machine-learning approach based on 24 independent bacterial data sets comprising 758 samples and 22 independent fungal data sets comprising 279 samples of healthy or Fusarium wilt-diseased soils from eight different countries. We found that soil bacterial and fungal communities were both clearly separated between diseased and healthy soil samples that originated from six crops across nine countries or regions. Alpha diversity was consistently greater in the fungal community of healthy soils. While diseased soil microbiomes harbored higher abundances of Xanthomonadaceae , Bacillaceae , Gibberella , and Fusarium oxysporum , the healthy soil microbiome contained more Streptomyces Mirabilis , Bradyrhizobiaceae , Comamonadaceae , Mortierella , and nonpathogenic fungi of Fusarium . Furthermore, a random forest method identified 45 bacterial OTUs and 40 fungal OTUs that categorized the health status of the soil with an accuracy >80%. We conclude that these models can be applied to predict the potential for occurrence of F. oxysporum wilt by revealing key biological indicators and features common to the wilt-diseased soil microbiome.

Detectability of morphs in different light environments is one of the mechanisms favoring the persistence of color polymorphism via disruptive selection. This mechanism predicts that different morphs should be more active and successful when light conditions make them more cryptic. In nocturnal birds, no study has analyzed yet whether morphs show a different degree of nocturnality, showing different circadian activity rhythms in relation to night and day light. We analyze activity patterns and hunting efficiency of color morphs in relation to day/night light in the nocturnal polymorphic scops owl (Otus scops). Forty-four percent of owl activity took place in the first hours after sunrise and before sunset. Also, we found that nocturnal activity decreased from grey to brown females and that grey males fed their chicks more than brown ones at night. Visual modeling revealed that grey individuals would be more conspicuous to their prey than brownish ones during the day. These findings suggest that part of the activity of nocturnal scops owls may occur during the day and that grey individuals would be better adapted to forage during night-light than brownish ones. However, brown morphs seemed not to be better adapted to forage at day, suggesting that other mechanisms than visual detection by predators or prey contribute to the persistence of color polymorphism in the species.Significance statementCircadian activity patterns can vary intraspecifically in response to changing environmental conditions. Color variants in polymorphic species could change their circadian activity rhythms differently in relation to diel luminal variation, switching from nocturnality to diurnality or vice versa, to achieve better background matching. We study for the first time whether different color variants of the nocturnal polymorphic scops owl (Otus scops) show different circadian activity rhythms with respect to night and day light conditions by relying on GPS-tracking data and nest video recordings. We also use perceptual visual modeling to study crypsis of morphs during the day. We found that nearly half of the activity of owls took place in the first hours after sunrise and before sunset. Also, we found that grey individuals would be better adapted to forage during night-light than more brownish ones probably due to their poor background matching during the day for the visual system of insects. These results support the idea that in scops owls, color morphs may show different degree of nocturnality to improve their crypsis.

We present the complete genome sequence of an aviadenovirus obtained by metagenomics from cloacal swabs taken from a free-living Eurasian scops owl (Otus scops, a small raptor distributed in Europe and several parts of Asia) in China. Thirty protein coding genes were predicted in this 40,239-bp-long genome, which encodes the largest fiber protein among all reported aviadenoviruses. The viral genome sequence is highly divergent, and the encoded proteins have an average of only 55% amino acid sequence identity to those of other adenoviruses. In phylogenetic analysis, the new owl virus grouped with members of the genus Aviadenovirus and formed a common clade with another owl adenovirus reported previously in Japan. This is the second complete genome sequence of an aviadenovirus discovered in owls, and its proteins have an average of 62% amino acid sequence identity to those of the previously reported owl adenovirus. Combining this result with comparative genomic analysis of all aviadenoviruses, we propose that this owl virus and the previously described Japanese owl adenovirus can be assigned to two new species in the genus Aviadenovirus. This study provides new data on the diversity of aviadenoviruses in wild birds.

Toxoplasma gondii is a zoonotic intracellular protozoan parasite of worldwide distribution that infects many species of warm-blooded animals, including birds. To date, there is scant information about the seropositivity of T. gondii and the risk factors associated with T. gondii infection in wild bird populations. In the present study, T. gondii infection was evaluated on sera obtained from 1079 wild birds belonging to 56 species (including Falconiformes (n = 610), Strigiformes (n = 260), Ciconiiformes (n = 156), Gruiformes (n = 21), and other orders (n = 32), from different areas of Spain. Antibodies to T. gondii (modified agglutination test, MAT titer ≥1:25) were found in 282 (26.1%, IC95%:23.5–28.7) of the 1079 birds. This study constitute the first extensive survey in wild birds species in Spain and reports for the first time T. gondii antibodies in the griffon vulture (Gyps fulvus), short-toed snake-eagle (Circaetus gallicus), Bonelli's eagle (Aquila fasciata), golden eagle (Aquila chrysaetos), bearded vulture (Gypaetus barbatus), osprey (Pandion haliaetus), Montagu's harrier (Circus pygargus), Western marsh-harrier (Circus aeruginosus), peregrine falcon (Falco peregrinus), long-eared owl (Asio otus), common scops owl (Otus scops), Eurasian spoonbill (Platalea leucorodia), white stork (Ciconia ciconia), grey heron (Ardea cinerea), common moorhen (Gallinula chloropus); in the International Union for Conservation of Nature (IUCN) “vulnerable” Spanish imperial eagle (Aquila adalberti), lesser kestrel (Falco naumanni) and great bustard (Otis tarda); and in the IUCN “near threatened” red kite (Milvus milvus). The highest seropositivity by species was observed in the Eurasian eagle owl (Bubo bubo) (68.1%, 98 of 144). The main risk factors associated with T. gondii seropositivity in wild birds were age and diet, with the highest exposure in older animals and in carnivorous wild birds. The results showed that T. gondii infection is widespread and can be at a high level in many wild birds in Spain, most likely related to their feeding behaviour.

Aim: Our specific objectives were to (a) estimate detection probabilities of nocturnalbird species, after taking into account survey-specific covariates, and (b) investigatethe influence of site-specific covariates on owl and nightjar abundance, integratingeffects of imperfect detection.Innovation: We conceived a survey protocol to estimate probabilities of detectionand estimates of abundance of owls and nightjars in a large area, the Basque Country,northern Spain.Main Conclusions: Our results show that detection probability was strongly influ-enced by playback broadcast and by observer experience. Date irregularly affectedspecies according to their reproductive periods, and we also found that vocal activitygradually diminished proportionally to the hour after sunset. Tawny owl (Strix aluco)was the most abundant and widely distributed species. Its abundance was positivelyrelated to forest areas (mainly pine timber forests) and decreased in large urban andagricultural areas. Open space species were less common. Barn owls (Tyto alba), littleowls (Athene noctua), Eurasian scops owls (Otus scops) and long-eared owls (Asio otus)avoided forest areas, but showed different responses to agriculture, grass-fields,scrub and urban areas. Finally, European nightjar (Caprimulgus europaeus) was mod-erately frequent, and its abundance was favoured by scrub areas and, weakly, by eu-calyptus patches, whereas it was negatively affected by large forest areas. We haveshown that it is fundamental to consider the effects of survey-specific covariates inthe methodology design and analytical development. Our results also indicate someecological adaptations and population changes in the nocturnal bird community fol-lowing an increase in urbanization and in the extent of timber plantations, and alsothe simplification of natural habitats

Species demanding specific habitat requirements suffer, particularly under environmental changes. The smallest owl of Africa, the Sokoke Scops Owl (Otus ireneae), occurs exclusively in East African coastal forests. To understand the movement behaviour and habitat demands of O. ireneae, we combined data from radio-tracking and remote sensing to calculate Species Distribution Models across the Arabuko Sokoke forest in southern Kenya. Based on these data, we estimated the local population size and projected the distribution of current suitable habitats. We found that the species occurs only in Cynometra woodland with large old trees and dense vegetation. Based on home range sizes and the distribution of suitable forest habitats, the local population size was estimated at < 400 pairs. Ongoing selective logging of hard-wood trees and the production of charcoal are reducing habitat quality of which will reduce the low numbers of O. ireneae, and of other specialist forest species, even further. Due to their close connection with intact Cynometra forest, O. ireneae is an excellent indicator of intact forest remnants. In addition, this species is a suitable flagship for the promotion and conservation of the last remaining coastal forests of East Africa.