Passive acoustic monitoring has proven to have many advantages for monitoring efforts and research activities. However, there are considerations to be taken into account regarding the placement of autonomous sound recorders. Detection ranges differ among species and in response to variable conditions such as weather or the location of vocalising animals. It is thus important to the success of a research project to understand, with a certain degree of confidence, the distances at which birds might be detected. In two types of forests in Poland, we played back the vocalisations of 31 species of European forest birds exemplifying different singing characteristics. Based on recordings obtained along a 500-m transect, we estimated the probability of detection and maximum detection distance of each vocalisation. We broadcasted the recording at three heights of singing and repeated playbacks three times during the breeding season to evaluate the effect of vegetation growth. Our results revealed that environmental and meteorological factors had a significant influence on both detection probability and maximum detection distances. This work provides comprehensive measurements of detection distance for 31 bird species and can be used to plan passive acoustic monitoring research in Europe, taking into account species traits and individual characteristics of the study area.

In the early morning, large groups of up to hundreds or even thousands of roosting birds, sometimes comprising the entire roost population, often take off together in sudden mass departures. These departures commonly occur in low-light conditions and structurally complex habitats where access to visual cues is likely to be restricted. Roosting birds are often highly vocal, leading us to hypothesise that vocalisations, which can propagate over large distances, could provide a means of enabling individuals to agree on when to depart - that is to establish a consensus1 - and thus coordinate the timing of mass movements. Investigations of the role of acoustic signals in coordinating collective decisions have been limited to honeybees2 and relatively small vertebrate groups (<50 individuals)3-5 and have rarely included experimental validation2,3. Here, by combining field recordings with a large-scale experimental manipulation, we show that jackdaws (Corvus monedula) use vocalisations to coordinate mass departures from winter roosts. This provides empirical evidence for vocally-mediated consensus decision-making in large vertebrate groups.

Our current understanding of the natural evolution of RNA viruses comes largely from consensus level genetic analyses which ignore the diverse mutant swarms that comprise within-host viral populations. The breadth and composition of viral mutant swarms impact viral fitness and adaptation, and the capacity for swarm plasticity is likely to be particularly important for arthropod-borne viruses (arboviruses) that cycle between taxonomically divergent hosts. Despite this, characterization of the relationship between the selective pressures and genetic signatures of the mutant swarm and consensus sequences is lacking. To clarify this, we analyzed previously generated whole genome, deep-sequencing data from 548 West Nile virus samples isolated from avian tissues or mosquitoes in New York State from 1999-2018. Both consensus level (interhost) and minority level (intrahost) nucleotide and amino acid sequences were analyzed, and diversity at each position was calculated across the genome in order to assess the relationship between minority and consensus sequences for individual genes and hosts. Our results indicate that consensus sequences are an inept representation of the overall genetic diversity. Unique host and gene-specific signatures and selective pressures were identified. These data demonstrate that an accurate and comprehensive understanding of arbovirus evolution and adaptation within and between hosts requires consideration of minority genotypes.

The expansion of overhead power lines worldwide challenges companies of energy transmission and distribution, regulators and environmental consultants, among other stakeholders, to effectively mitigate their negative impacts on wildlife. Wire-marking is currently the most widespread and recommended measure to reduce bird collisions with these infrastructures. Nevertheless, and despite its importance for a bird-friendly development of energy projects, there is still much uncertainty about what explains wire-marking effectiveness. We performed an extensive literature review and meta-analysis to evaluate the overall effectiveness of wire-marking in reducing bird collisions with power lines, including the possible influencing factors of power line voltage, habitat and type of device. We gathered data from 35 field studies across the world (which included 66 trials) assessing the effectiveness of wire-marking based on regular carcass searches beneath power lines. Overall, wire-marking reduced bird collisions with power lines by half (50.4%; 95% Confidence Interval Estimate: 40.4-58.8%), although this estimate of effectiveness is lower than the one reported in a meta-analysis performed in 2011. Despite the effort to include both peer-reviewed and grey literature studies in the present meta-analysis, the risk of publication bias could not be entirely excluded and may be still overestimating the true overall effect of wire-marking. High heterogeneity among the study outcomes hindered the power to detect clear moderating effects, with none of explanatory variables being statistically significant. Large between-study heterogeneity is (to some extent) explained by the variety of anti-collision devices available, wire-marking intensities used and ecological circumstances in which the experiments were carried out. Nonetheless, it may be also related to within-study methodological biases and reporting gaps in the existing field studies. Robust experimental designs (ideally using Before-After-Control-Impact approaches), comprehensive reporting of results and broad dissemination of study findings are needed to increase the statistical power of future meta-analyses. Ways to achieve these improvements in field studies are presented in detail. Their inclusion in future meta-analyses will increase the knowledge on the drivers of wire-marking effectiveness, which is critical to better inform decision-making processes and environmental management plans.

Feathers are widely used to represent mercury contamination in birds. Yet, few recommendations exist that provide guidance for using bird feathers in mercury monitoring programs. We conducted a literature review and 5 experiments to show that mercury concentrations vary substantially within (vane >100% higher than calamus) and among (>1000%) individual feathers from the same bird. We developed a research tool and guidelines for using bird feathers for mercury studies based on 3 components: 1) variability of feather mercury concentrations within an individual bird (coefficient of variation), 2) desired accuracy of the measured mercury concentration, and 3) feather and bird mass. Our results suggest a general rule that if the goal is to limit analytical and processing costs by using whole feathers in only one sample boat, then to achieve an accuracy within 10% of a bird\'s overall average feather mercury concentration a bird with a coefficient of variation ≤10% must be <190 g (size of a large shorebird). To achieve an accuracy within 20%, a bird with a coefficient of variation ≤10% must be <920 g (a large duck). When more than one sample boat is needed to fit the required number of feathers to achieve the desired accuracy, the results suggest homogenizing feathers and analyzing an aliquot of ≥20 mg for mercury. The present study suggests increasing the number of feathers typically used per bird to assess mercury concentrations. Environ Toxicol Chem 2019;38:1164-1187. Published 2019 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

BACKGROUND: Repeat elements are important components of most eukaryotic genomes. Most existing tools for repeat analysis rely either on high quality reference genomes or existing repeat libraries. Thus, it is still challenging to do repeat analysis for species with highly repetitive or complex genomes which often do not have good reference genomes or annotated repeat libraries. Recently we developed a computational method called REPdenovo that constructs consensus repeat sequences directly from short sequence reads, which outperforms an existing tool called RepARK. One major issue with REPdenovo is that it doesn\'t perform well for repeats with relatively high divergence rates or low copy numbers. In this paper, we present an improved approach for constructing consensus repeats directly from short reads. Comparing with the original REPdenovo, the improved approach uses more repeat-related k-mers and improves repeat assembly quality using a consensus-based k-mer processing method.
RESULTS: We compare the performance of the new method with REPdenovo and RepARK on Human, Arabidopsis thaliana and Drosophila melanogaster short sequencing data. And the new method fully constructs more repeats in Repbase than the original REPdenovo and RepARK, especially for repeats of higher divergence rates and lower copy number. We also apply our new method on Hummingbird data which doesn\'t have a known repeat library, and it constructs many repeat elements that can be validated using PacBio long reads.
CONCLUSIONS: We propose an improved method for reconstructing repeat elements directly from short sequence reads. The results show that our new method can assemble more complete repeats than REPdenovo (and also RepARK). Our new approach has been implemented as part of the REPdenovo software package, which is available for download at https://github.com/Reedwarbler/REPdenovo .

Recent developments in phylogenetic methods and data acquisition have allowed for the construction of large and comprehensive phylogenetic relationships. Published phylogenies represent an enormous resource that not only facilitates the resolution of questions related to comparative biology, but also provides a resource on which to gauge the development of concordance across the tree of life. From the Open Tree of Life, we gathered 290 avian phylogenies representing all major groups that have been published over the last few decades and analyzed how concordance and conflict develop among these trees through time. Nine large scale phylogenetic hypotheses (including a new synthetic tree from this study) were used for comparisons. We found that conflicts were over-represented both along the backbone (higher-level neoavian relationships) and within the oscine Passeriformes. Importantly, although we have made major strides in the resolution of major clades, recent published comprehensive trees, as well as trees of individual clades, continue to contribute significantly to the resolution of relationships throughout the avian phylogeny. Our analyses highlight the need for continued research into the resolution of avian relationships.

Since the publication of the Organisation for Economic Co-operation and Development (OECD) avian acute oral guideline, OECD 223, empirical data have become available to compare the performance of OECD 223 with statistical simulations used to validate this guideline and with empirical data for US Environmental Protection Agency Office of Chemical Safety and Pollution Prevention (USEPA OCSPP) guideline OCSPP 850.2100. Empirical studies comprised 244 for Northern bobwhite, of which 73 were dose-response tests and 171 were limit tests. Of the dose-response tests, 26 were conducted to OECD 223 (using 3-4 stages) and 33 to OCSPP 850.2100 (using the single 50-bird design). Data were collected from 5 avian testing laboratories from studies performed between 2006 and 2013. The success with which the LD50 and slope could be determined was 100% and 96% for OECD 223 (mean 26 birds per test) and 100% and 51% for OCSPP 850.2100 (mean 50 birds per test). This was consistent with the statistical simulations. Control mortality across all species and designs amounted to 0.26% (n = 2655) with only single mortalities occurring in any 1 study and <1% for any 1 species. The simulations used to validate the OECD 223 design showed that control mortality up to 1% will have no observable impact on the performance. The distribution of time to death for Northern bobwhite, zebra finch, and canary were obtained from 90, 29, and 17 studies, and mortalities appeared within 3 d for 71%, 95%, and 91% of birds tested, respectively. Integr Environ Assess Manag 2017;13:906-914. © 2017 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

This paper considers the consensus behavior of a spatially distributed 3-D dynamical network composed of heterogeneous agents: leaders and followers, in which the leaders have the preferred information about the destination, while the followers do not have. All followers move in a 3-D Euclidean space with a given speed and with their headings updated according to the average velocity of the corresponding neighbors. Compared with the 2-D model, a key point lies in how to analyze the dynamical behavior of a \"linear\" nonhomogeneous equation where the nonhomogeneous term strongly nonlinearly depends on the states of all agents. Using the network structure and the estimation of some characteristics for the initial states, we present a proper decaying rate for the nonhomogeneous term and then establish lower bounds on the ratio of the number of leaders to the number of followers that is needed for the expected consensus by considering two cases: 1) fixed speed and neighborhood radius and 2) variable speed and neighborhood radius with respect to the population size. Some simulation examples are given to justify the theoretical results.This paper considers the consensus behavior of a spatially distributed 3-D dynamical network composed of heterogeneous agents: leaders and followers, in which the leaders have the preferred information about the destination, while the followers do not have. All followers move in a 3-D Euclidean space with a given speed and with their headings updated according to the average velocity of the corresponding neighbors. Compared with the 2-D model, a key point lies in how to analyze the dynamical behavior of a \"linear\" nonhomogeneous equation where the nonhomogeneous term strongly nonlinearly depends on the states of all agents. Using the network structure and the estimation of some characteristics for the initial states, we present a proper decaying rate for the nonhomogeneous term and then establish lower bounds on the ratio of the number of leaders to the number of followers that is needed for the expected consensus by considering two cases: 1) fixed speed and neighborhood radius and 2) variable speed and neighborhood radius with respect to the population size. Some simulation examples are given to justify the theoretical results.

BACKGROUND: West Nile virus (WNV) is a zoonotic mosquito-borne virus with a broad host range that infects mainly birds and mosquitos, but also mammals (including humans), reptiles, amphibians and ticks. It is maintained in a bird-mosquito-bird transmission cycle. The most important vectors are bird-feeding mosquitos of the Culex genus; maintenance and amplification mainly involve passerine birds. WNV can cause disease in humans, horses and several species of birds following infection of the central nervous system.
UNASSIGNED: Cats can also be infected through mosquito bites, and by eating infected small mammals and probably also birds. Although seroprevalence in cats can be high in endemic areas, clinical disease and mortality are rarely reported. If a cat is suspected of clinical signs due to an acute WNV infection, symptomatic treatment is indicated.