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592 results for “songbirds”
A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird
<p>The dark-eyed junco (<i>Junco hyemalis</i>) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior and evolutionary biology for over a century. It is composed by at least six distinct, geographically structured forms of recent evolutionary origin presenting remarkable variation in phenotypic traits, migratory behavior and habitat. Here we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago<sup>TM</sup> and Dovetail HiC<sup>TM</sup> libraries. The final assembly is 1,031,523,571 bp long, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71,3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. Genome assembly and annotated set of genes yielded 95.4% and 96.2% completeness scores, respectively, when compared with the BUSCO avian dataset. This new assembly for <i>J. hyemalis </i>provides a valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.</p>
Data from: Maintenance of local adaptation despite gene flow in a coastal songbird
<p class="MsoNormal">Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (<em>Melospiza melodia</em>) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (<em>M. m. atlantica</em>), a coastal specialist; and the eastern song sparrow (<em>M. m. melodia</em>), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment (IBE), not isolation by distance (IBD). A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.</p>
Lack of avian predators is associated with behavioural plasticity in nest construction and height in an island songbird
<p>Orange-crowned warblers, Leiothlypis celata sordida, breeding on the California Channel Islands exhibit remarkable variation in their nest structure and placement, providing an intriguing exception to the general pattern that avian nest structure and nest site selection are highly conserved characters. We examined nest construction at both the population and individual scale to test whether warblers on Santa Catalina Island change their nest construction in response to nest height. At the population level, warblers built both lighter, grass-dominated ground nests and heavier off-ground nests that contained more ridged materials and less grass. The probability of nest success was significantly and positively correlated with nest height. At the individual level, we found the same individuals were capable of building on- and off-ground nests between nesting attempts within the same season. However, nest construction was highly variable among individuals and not significantly correlated with nest success after controlling for nest height. We suggest this observed behavioural plasticity in nest construction and nest height is a hierarchical response to the absence of avian predators. Reduced risk from avian predators appears to allow the warblers to use a variety of nest sites, thereby necessitating increased flexibility in nest construction.</p>
Impacts of oil well drilling and operating noise on abundance and productivity of grassland songbirds
<p>Anthropogenic noise from natural resource extraction may negatively impact many species, particularly those reliant on acoustic communication. To compare impacts of several types of noise resulting from oil extraction operations on habitat use and productivity of grassland songbirds, we designed and implemented a novel large-scale, spatially and temporally replicated experiment. <br>We recreated soundscapes produced by drilling and operating oil well noise, and compared impacts of noise-producing and quiet playback infrastructure, in twenty-nine 64.7-ha native prairie sites in Alberta, Canada, from 2013–2015. Drilling noise recordings played 24 hours/day for 10 days, twice during each breeding season, while oil well operating noise played continuously, 24 hours/day, throughout each ~90-day breeding season. <br>Despite the much shorter duration of drilling noise playbacks, drilling noise negatively impacted three of our four focal species, and had a much greater impact on habitat use and productivity than did well operating noise. Infrastructure also impacted Vesper Sparrows and Sprague's Pipits, even in the absence of noise. <br>Synthesis and applications: Acute oil drilling noise had a greater negative impact on breeding migratory birds when compared to chronic oil well noise, perhaps because drilling noise is unpredictable. While this study demonstrates that noise alone can negatively impact habitat use, nesting success, and nestling quality, it is also clear that effective mitigation strategies require both noise and above-ground infrastructure management to reduce impacts on wildlife.</p>
Plasticity in female timing may explain earlier breeding in a North American songbird
<p>Many species have shifted their breeding phenology in response to climate change. Identifying the magnitude of phenological shifts and whether climate-mediated selection drives these shifts is key for determining species' resilience to climate change. Birds are a strong model for studying phenological shifts due to numerous long-term research studies; however, generalities pertaining to drivers of phenological shifts will emerge only as we add study species that differ in life history and geography. We investigated 32 years of reproductive timing in a non-migratory population of dark-eyed juncos (Junco hyemalis). We predicted that plasticity in reproductive timing would allow females to breed earlier in warmer springs. We also predicted that selection would favour earlier breeding, and we asked whether temperatures throughout the breeding season would predict the strength of selection. To test these predictions, we examined temporal changes in the annual median date for reproductive onset (i.e., first egg date), and we used a sliding window analysis to identify monthly spring temperatures driving these patterns. Next, we explored plasticity in reproductive timing and asked whether selection favoured earlier breeding. Lastly, we used a sliding window analysis to identify the time during the breeding season that temperature was most associated with selection favouring earlier breeding. First egg dates occurred earlier over time and strongly covaried with April temperatures. Further, for individual females that bred in more than one year, they typically bred earlier in warmer Aprils, exhibiting plastic responses to April temperature. We also found significant overall selection favouring earlier breeding (i.e., higher relative fitness with earlier first egg dates) and variation in selection for earlier breeding over time. However, temperature across diverse climatic windows did not predict the strength of selection. Our findings provide further evidence for the role of phenotypic plasticity in shifting phenology in response to earlier springs. We provide evidence for the role of selection favouring earlier breeding, regardless of temperature, thus setting the stage for adaptive changes in female breeding phenology. We suggest for multi-brooded birds that advancing first egg dates likely increases the length of the breeding season, and therefore, reproductive success.</p>
Data for: Telomere length predicts timing and intensity of migratory behavior in a nomadic songbird
<p>Our understanding of state-dependent behavior is reliant on identifying physiological indicators of condition. Telomeres are of growing interest for understanding behavior as they capture differences in biological state and residual lifespan. To understand the significance of variable telomere lengths for behavior and test two hypotheses describing the relationship between telomeres and behavior (i.e., the causation and the selective adoption hypotheses), we assessed if telomere lengths are longitudinally repeatable traits related to spring migratory behavior in captive pine siskins (<em>Spinus pinus</em>). Pine siskins are nomadic songbirds that exhibit highly flexible, facultative migrations, including a period of spring nomadism. Captive individuals exhibit extensive variation in spring migratory restlessness and are an excellent system for mechanistic studies of migratory behavior. Telomere lengths were found to be significantly repeatable (R = 0.51) over 4 months, and shorter pre-migratory telomeres were associated with earlier and more intense expression of spring nocturnal migratory restlessness. Telomere dynamics did not vary with migratory behavior. Our results describe the relationship between telomere length and migratory behavior and provide support for the selective adoption hypothesis. More broadly, we provide a novel perspective on the significance of variable telomere lengths for animal behavior and the timing of annual cycle events.</p>
A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds
<p><span>We report the discovery of a novel neo-sex chromosome in an African warbler, <em>Sylvietta brachyura</em> (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome–sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single-species representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae, and Leiothrichidae). In all three species, we confirmed the translocation of a part of chromosome 4A to the sex chromosomes, which originated basally in Sylvioidea. In <em>S. brachyura</em>, we found that a part of chromosome 8 has been translocated to the sex chromosomes, forming a unique neo-sex chromosome in this lineage. Furthermore, the non-recombining part of 4A in <em>S. brachyura</em> is smaller than in other Sylvioidea species which suggests that recombination continued along this region after the fusion event in the Sylvioidea ancestor. These findings reveal additional sex chromosome diversity among the Sylvioidea, where five separate translocation events are now confirmed.</span></p>
Data for: Two is better than one: Coupling DNA metabarcoding and stable isotope analysis improves dietary characterizations for a riparian-obligate, migratory songbird
<p>While an increasing number of studies are adopting molecular and chemical methods for dietary characterization, these studies often employ only one of these laboratory-based techniques; an approach which may yield an incomplete, or even biased, understanding of diet due to each method's inherent limitations. To explore the utility of coupling molecular and chemical techniques for dietary characterizations, we applied DNA metabarcoding alongside stable isotope analysis to characterize the dietary niche of breeding Louisiana waterthrush (<em>Parkesia motacilla</em>), a migratory songbird hypothesized to preferentially provision their offspring with pollution-intolerant, aquatic arthropod prey. While DNA metabarcoding was unable to determine if waterthrush provision aquatic and terrestrial prey in different abundances, we found that specific aquatic taxa were more likely to be detected in successive seasons than their terrestrial counterparts, thus supporting the aquatic specialization hypothesis. Our isotopic analysis added greater context to this hypothesis by concluding that breeding waterthrush provisioned Ephemeroptera and Plecoptera, two pollution-intolerant, aquatic orders, in higher quantities than other prey groups, and expanded their functional trophic niche when such prey were not abundantly provisioned. Finally, we found that the dietary characterizations from each approach were often uncorrelated, indicating that the results gleaned from a diet study can be particularly sensitive to the applied methodologies. Our findings contribute to a growing body of work indicating the importance of high-quality, aquatic habitats for both consumers and their pollution-intolerant prey, while also demonstrating how the application of multiple, laboratory-based techniques can provide insights not offered by either technique alone.</p>
Do departure and flight route decisions correlate with immune parameters in migratory songbirds?
<p>Many songbirds migrate twice a year to exploit seasonally available resources. These journeys are energetically demanding and the energy reserves of these small birds are limited. Accordingly, most of the time migrating is spent during stopovers that serve to rest, replenish resources and recover. While external influences, like prevailing weather conditions and resource availability, are well studied with regard to stopover behavior and departure decisions, studies on how birds' individual physiological conditions and stopover decisions may be linked are scarce.</p> <p>We used a large-scale radio-telemetry network covering the German Bight (SE North Sea) to study how birds' immunological constitution at stopover may correlate with departure and flight behavior in five species of short- to medium-distance migratory songbirds. We measured markers of the innate (bacterial killing activity, lysozyme concentration, natural antibodies, and complement titers) and acquired immune function (immunoglobulin Y) in the birds' plasma. After sampling, we tracked the birds' behavior in terms of stopover duration as well as flight routes and flight distances within the telemetry network after departure.</p> <p>We found that stopover durations were positively related to natural antibodies and immunoglobulin Y across species and to the bacterial killing ability solely in song thrushes in spring, while no relations became apparent in fall. Flight distances were linked positively to immunoglobulin Y concentrations in both spring and fall, though not in all of the investigated species. Coastal and offshore-oriented routes were taken independent of the birds' immune status.</p> <p>Our study for the first time shows that the migratory behavior of songbirds in the wild is correlated with their immune status, not only during but also beyond stopover. Further, birds with increased complement titers and Immunoglobulin Y concentrations, either due to recent infection or greater investment in their immune function, took additional time at their stopover sites, probably to reach their breeding grounds in good condition. During the less time-constrained fall season, stopovers were generally prolonged, independent from the birds' immune status, and any delays taken to improve immune status are most likely not detrimental in terms of fitness.</p>
Data from: The effect of environmental variation on the relationship between survival and risk-taking behaviour in a migratory songbird
<p>Temporal changes in environmental conditions may play a major role in the year-to-year variation in fitness consequences of behaviours. Identifying environmental drivers of such variation is crucial to understand the evolutionary trajectories of behaviours in natural contexts. However, our understanding of how environmental variation influences behaviours in the wild remains limited. Using data collected over 14 breeding seasons from a collared flycatcher (<em>Ficedula albicollis</em>) population, we examined the effect of environmental variation on the relationship between survival and risk-taking behaviour, a highly variable behavioural trait with great evolutionary and ecological significance. Specifically, using annual recapture probability as a proxy of survival, we evaluated the specific effect of predation pressure, food availability and mean temperature on the relationship between annual recapture probability and risk-taking behaviour (measured as flight initiation distance, FID). We found a negative trend, as the relationship between annual recapture probability and FID decreased over the study years, and changed from positive to negative. Specifically, in the early years of the study, risk-avoiding individuals exhibited a higher annual recapture probability, whereas in the later years, risk-avoiders had a lower annual recapture probability. However, we did not find evidence that any of the considered environmental factors mediated the variation in the relationship between survival and risk-taking behaviour.</p>
Bioacoustic monitoring reveals shifts in breeding songbird populations and singing behaviour with selective logging in tropical forests
<b>Description: </b><p>Counts of individual male songbirds, males and females, songs and duets and original WAV audio recordings used to generate them</p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/131"><b>Population and behavioral responses of songbirds to logging and rain forest fragmentation</b></a></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=3366104">here</a></p><p><b>Files: </b>This dataset consists of 13 files: Pillay_et_al_Songbirds_Acoustic_Counts_Vegetation_Cover.xlsx, 2013_B.zip, 2013_D.zip, 2013_E.zip, 2013_F.zip, 2013_OG1.zip, 2013_OG2.zip, 2014_B.zip, 2014_D.zip, 2014_E.zip, 2014_F.zip, 2014_OG1.zip, 2014_OG2.zip</p><p><b>Pillay_et_al_Songbirds_Acoustic_Counts_Vegetation_Cover.xlsx</b></p><p>This file contains dataset metadata and 5 data tables:</p><ol><li><p><b>CountsMale</b> (described in worksheet CountsMale)</p><p>Description: Counts of male individuals of songbird species</p><p>Number of fields: 12</p><p>Number of data rows: 5700</p><p>Fields: </p><ul><li><b>year</b>: Year of Survey (Field type: id)</li><li><b>ftype</b>: Forest Type (Field type: categorical)</li><li><b>block</b>: Unique ID of Blocks within which Sampling Plots are located (Field type: id)</li><li><b>location</b>: Unique ID of Sampling Plots (Field type: location)</li><li><b>fragment</b>: Future fragments within which sampling plots in logged forest plots were located; not applicable for unlogged forest plots (Field type: id)</li><li><b>species</b>: Species Identity (Field type: taxa)</li><li><b>day</b>: Days 1 to 2 of sampling in each plot (Field type: numeric)</li><li><b>date</b>: Date of Sampling (Field type: date)</li><li><b>jul.date</b>: Julian Date of Sampling (Field type: numeric)</li><li><b>time1-6AM</b>: Counts of male individuals for 6:00-6:05 AM; detection histories generated by collapsing counts to 1/0 data (Field type: numeric)</li><li><b>time2-7AM</b>: Counts of male individuals for 7:00-7:05 AM; detection histories generated by collapsing counts to 1/0 data (Field type: numeric)</li><li><b>time3-8AM</b>: Counts of male individuals for 8:00-8:05 AM; detection histories generated by collapsing counts to 1/0 data (Field type: numeric)</li></ul></li><li><p><b>CountsMaleFemale</b> (described in worksheet CountsMaleFemale)</p><p>Description: Counts of male plus female individuals of songbird species</p><p>Number of fields: 12</p><p>Number of data rows: 1000</p><p>Fields: </p><ul><li><b>year</b>: Year of Survey (Field type: id)</li><li><b>ftype</b>: Forest Type (Field type: categorical)</li><li><b>block</b>: Unique ID of Blocks within which Sampling Plots are located (Field type: id)</li><li><b>location</b>: Unique ID of Sampling Plots (Field type: location)</li><li><b>fragment</b>: Future fragments within which sampling plots in logged forest plots were located; not applicable for unlogged forest plots (Field type: id)</li><li><b>species</b>: Species Identity (Field type: taxa)</li><li><b>day</b>: Days 1 to 2 of sampling in each plot (Field type: numeric)</li><li><b>date</b>: Date of Sampling (Field type: date)</li><li><b>jul.date</b>: Julian Date of Sampling (Field type: numeric)</li><li><b>time1-6AM</b>: Counts of male and female individuals for 6:00-6:05 AM; detection histories generated by collapsing counts to 1/0 data (Field type: numeric)</li><li><b>time2-7AM</b>: Counts of male and female individuals for 7:00-7:05 AM; detection histories generated by collapsing counts to 1/0 data (Field type: numeric)</li><li><b>time3-8AM</b>: Counts of male and female individuals for 8:00-8:05 AM; detection histories generated by collapsing counts to 1/0 data (Field type: numeric)</li></ul></li><li><p><b>CountsSong</b> (described in worksheet CountsSong)</p><p>Description: Counts of songs</p><p>Number of fields: 9</p><p>Number of data rows: 2850</p><p>Fields: </p><ul><li><b>year</b>: Year of Survey (Field type: id)</li><li><b>ftype</b>: Forest Type (Field type: categorical)</li><li><b>block</b>: Unique ID of Blocks within which Sampling Plots are located (Field type: id)</li><li><b>location</b>: Unique ID of Sampling Plots (Field type: location)</li><li><b>fragment</b>: Future fragments within which sampling plots in logged forest plots were located; not applicable for unlogged forest plots (Field type: id)</li><li><b>species</b>: Species Identity (Field type: taxa)</li><li><b>day3-6AM</b>: Counts of songs for 6:00-6:05 AM on day 3 or third consecutive day of sampling in each plot (Field type: numeric)</li><li><b>day3-7AM</b>: Counts of songs for 7:00-7:05 AM on day 3 or third consecutive day of sampling in each plot (Field type: numeric)</li><li><b>day3-8AM</b>: Counts of songs for 8:00-8:05 AM on day 3 or third consecutive day of sampling in each plot (Field type: numeric)</li></ul></li><li><p><b>CountsDuet</b> (described in worksheet CountsDuet)</p><p>Description: Counts of duets</p><p>Number of fields: 9</p><p>Number of data rows: 500</p><p>Fields: </p><ul><li><b>year</b>: Year of Survey (Field type: id)</li><li><b>ftype</b>: Forest Type (Field type: categorical)</li><li><b>block</b>: Unique ID of Blocks within which Sampling Plots are located (Field type: id)</li><li><b>location</b>: Unique ID of Sampling Plots (Field type: location)</li><li><b>fragment</b>: Future fragments within which sampling plots in logged forest plots were located; not applicable for unlogged forest plots (Field type: id)</li><li><b>species</b>: Species Identity (Field type: taxa)</li><li><b>day3-6AM</b>: Counts of duets for 6:00-6:05 AM on day 3 or third consecutive day of sampling in each plot (Field type: numeric)</li><li><b>day3-7AM</b>: Counts of duets for 7:00-7:05 AM on day 3 or third consecutive day of sampling in each plot (Field type: numeric)</li><li><b>day3-8AM</b>: Counts of duets for 8:00-8:05 AM on day 3 or third consecutive day of sampling in each plot (Field type: numeric)</li></ul></li><li><p><b>VegetationCover</b> (described in worksheet VegetationCover)</p><p>Description: Vegetation cover data</p><p>Number of fields: 6</p><p>Number of data rows: 50</p><p>Fields: </p><ul><li><b>location</b>: Unique ID of Sampling Plots (Field type: location)</li><li><b>forest.type</b>: Forest Type (Field type: categorical)</li><li><b>udens</b>: Proportion understory cover (Field type: numeric)</li><li><b>cc</b>: Proportion canopy cover (Field type: numeric)</li><li><b>can.ht</b>: Average canopy height (Field type: numeric)</li><li><b>max.canopy</b>: Maximum height of standing vegetation (Field type: numeric)</li></ul></li></ol><p><b>2013_B.zip</b></p><p>Description: WAV files from 2013 for site B</p><p><b>2013_D.zip</b></p><p>Description: WAV files from 2013 for site D</p><p><b>2013_E.zip</b></p><p>Description: WAV files from 2013 for site E</p><p><b>2013_F.zip</b></p><p>Description: WAV files from 2013 for site F</p><p><b>2013_OG1.zip</b></p><p>Description: WAV files from 2013 for site OG1</p><p><b>2013_OG2.zip</b></p><p>Description: WAV files from 2013 for site OG2</p><p><b>2014_B.zip</b></p><p>Description: WAV files from 2014 for site B</p><p><b>2014_D.zip</b></p><p>Description: WAV files from 2014 for site D</p><p><b>2014_E.zip</b></p><p>Description: WAV files from 2014 for site E</p><p><b>2014_F.zip</b></p><p>Description: WAV files from 2014 for site F</p><p><b>2014_OG1.zip</b></p><p>Description: WAV files from 2014 for site OG1</p><p><b>2014_OG2.zip</b></p><p>Description: WAV files from 2014 for site OG2</p><p><b>Date range: </b>2013-04-09 to 2014-07-26</p><p><b>Latitudinal extent: </b>4.6881 to 4.7530</p><p><b>Longitudinal extent: </b>116.9477 to 117.6249</p><p><b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.</p><div> -  Animalia <br> -  -  Chordata <br> -  -  -  Aves <br> -  -  -  -  Passeriformes <br> -  -  -  -  -  Timaliidae <br> -  -  -  -  -  -  <i>Stachyris</i> <br> -  -  -  -  -  -  -  <i>Stachyris maculata</i> <br> -  -  -  -  -  -  -  <i>Stachyris erythroptera</i> <br> -  -  -  -  -  -  -  <i>Stachyris poliocephala</i> <br> -  -  -  -  -  -  <i>Macronus</i> <br> -  -  -  -  -  -  -  <i>Macronus bornensis</i> <br> -  -  -  -  -  -  -  <i>Macronus ptilosus</i> (as synonym: <i>Macronous ptilosus</i>)<br> -  -  -  -  -  -  <i>Stachyridopsis</i> <br> -  -  -  -  -  -  -  <i>Stachyridopsis rufifrons</i> (as synonym: <i>Stachyris rufifrons</i>)<br> -  -  -  -  -  -  <i>Pomatorhinus</i> <br> -  -  -  -  -  -  -  <i>Pomatorhinus montanus</i> <br> -  -  -  -  -  Pellorneidae <br> -  -  -  -  -  -  <i>Trichastoma</i> <br> -  -  -  -  -  -  -  <i>Trichastoma bicolor</i> <br> -  -  -  -  -  -  <i>Alcippe</i> <br> -  -  -  -  -  -  -  <i>Alcippe brunneicauda</i> <br> -  -  -  -  -  -  <i>Pellorneum</i> <br> -  -  -  -  -  -  -  <i>Pellorneum capistratum</i> <br> -  -  -  -  -  -  <i>Malacocincla</i> <br> -  -  -  -  -  -  -  <i>Malacocincla malaccensis</i> <br> -  -  -  -  -  -  <i>Malacopteron</i> <br> -  -  -  -  -  -  -  <i>Malacopteron magnirostre</i> <br> -  -  -  -  -  -  -  <i>Malacopteron magnum</i> <br> -  -  -  -  -  -  -  <i>Malacopteron cinereum</i> <br> -  -  -  -  -  -  -  <i>Malacopteron affine</i> <br> -  -  -  -  -  Pycnonotidae <br> -  -  -  -  -  -  <i>Alophoixus</i> <br> -  -  -  -  -  -  -  <i>Alophoixus bres</i> <br> -  -  -  -  -  -  -  <i>Alophoixus phaeocephalus</i> <br> -  -  -  -  -  -  <i>Tricholestes</i> <br> -  -  -  -  -  -  -  <i>Tricholestes criniger</i> <br> -  -  -  -  -  -  <i>Iole</i> <br> -  -  -  -  -  -  -  <i>Iole olivacea</i> <br> -  -  -  -  -  -  <i>Pycnonotus</i> <br> -  -  -  -  -  -  -  <i>Pycnonotus atriceps</i> <br> -  -  -  -  -  -  -  <i>Pycnonotus simplex</i> <br> -  -  -  -  -  -  -  <i>Pycnonotus eutilotus</i> <br> -  -  -  -  -  -  -  <i>Pycnonotus brunneus</i> <br> -  -  -  -  -  -  -  <i>Pycnonotus erythropthalmos</i> <br> -  -  -  -  -  Stenostiridae <br> -  -  -  -  -  -  <i>Culicicapa</i> <br> -  -  -  -  -  -  -  <i>Culicicapa ceylonensis</i> <br> -  -  -  -  -  Muscicapidae <br> -  -  -  -  -  -  <i>Cyornis</i> <br> -  -  -  -  -  -  -  <i>Cyornis superbus</i> <br> -  -  -  -  -  -  -  <i>Cyornis unicolor</i> <br> -  -  -  -  -  -  <i>Rhinomyias</i> <br> -  -  -  -  -  -  -  <i>Rhinomyias umbratilis</i> <br> -  -  -  -  -  -  <i>Trichixos</i> <br> -  -  -  -  -  -  -  <i>Trichixos pyrropygus</i> <br> -  -  -  -  -  -  <i>Copsychus</i> <br> -  -  -  -  -  -  -  <i>Copsychus stricklandii</i> <br> -  -  -  -  -  Monarchidae <br> -  -  -  -  -  -  <i>Terpsiphone</i> <br> -  -  -  -  -  -  -  <i>Terpsiphone paradisi</i> <br> -  -  -  -  -  -  <i>Hypothymis</i> <br> -  -  -  -  -  -  -  <i>Hypothymis azurea</i> <br></div><p></p>
Direct evidence for nest predation by the edible dormouse (Glis glis, Rodentia) in open-cup nesting songbirds
<p>Here we provide the first direct evidence, with the use of time-lapse video surveillance, that edible dormouse (Glis glis), depredated eggs and nestlings of two open-nesting passerine species, the Eurasian blackcap (Sylvia atricapilla), and the common blackbird (Turdus merula) in a central European woodland. In the blackcap, we detected three predation events. In the first two cases, edible dormouse flushed away incubating/brooding females and preyed upon either the eggs or the nestlings. The third case documents egg predation on an abandoned nest. The fourth case (two files and b) documents an attempt to forage on eggs in an abandoned nest of song thrush (Turdus philomelos). Note that an Apodemus mouse brought an egg into this nest before. In the blackbird (files Case 5a,b), we document a single case of dormouse attacking a brooding female. The female and nestlings managed to escape. Our data bring another piece of evidence for dormice predation on Passerine birds and they highlight the value of direct nest surveillance for documenting rodent predatory impact on birds.</p> <p> </p> <p>File names match the order of the cases as desribed in the paper published in Journal of Vertebrate Biology <a href="https://doi.org/10.25225/jvb.24090">https://doi.org/10.25225/jvb.24090</a>. Files labelled as "edited" contain scenes with the predations events only.</p>
Social and abiotic factors differentially affect plumage ornamentation of young and old males in an Australian songbird
<p>Both abiotic environmental conditions and variation in social environment are known to impact the acquisition of sexual signals. However, the influences of abiotic environmental and social factors are rarely compared to each other. Here we test the relative importance of these factors in determining whether and when male red-backed fairywrens (<i>Malurus melanocephalus</i>) moult into a known sexual signal, ornamented breeding plumage. One-year-old male red-backed fairywrens vary in whether or not they acquire ornamentation, whereas males age two and older vary in their timing of ornament acquisition. It is unclear whether these processes are determined by the same or different factors and we examine both events using a combination of long-term breeding records and non-breeding social networks. We found that one-year-old males that paired prior to the start of the breeding season were more likely to acquire ornamented plumage, but rainfall did not influence whether one-year-old males acquired ornamented plumage. Thus, for young individuals, social cues appear to play a larger role than abiotic environmental factors in determining ornament acquisition. For older males, timing of ornamented plumage acquisition was constrained by rainfall, with drier non-breeding seasons leading to poorer physiological condition and later moult dates. Thus, sexual signal variation in older males appears to be a condition-dependent trait, driven by abiotic environmental and physiological factors rather than social cues. These findings reveal that factors influencing sexual signal expression can vary with age when age classes exhibit different forms of signal variation. Our results suggest that social environment may drive sexual signal variation in young individuals, whereas abiotic environmental variation may drive sexual signal variation in older individuals.</p>
Local timing of rainfall predicts the timing of moult within a single locality and the progress of moult among localities that vary in the onset of the wet season in a year-round breeding tropical songbird
<p>Rainfall seasonality is likely an important cue for timing key annual cycle events like moult in birds living in seasonally arid environments, but its precise effect is difficult to establish because seasonal rainfall may affect other covarying annual events such as breeding in the same way. In central Nigeria, however, Common Bulbuls <em>Pycnonotus barbatus</em> moult in the wet season but only show weak breeding seasonality. This suggests that moult is more sensitive to rainfall than breeding, but a similar outcome is possible if moult is simply periodic. We tested the relationship between rainfall and moult in Common Bulbuls at a single location over 18 years: on average moult started 5th May (± 41 days: 25th March–15th June), being on average later than the onset of the rains which is usually mid-April. The likelihood of finding a moulting Common bulbul was best predicted by rainfall 9–15 weeks before moult was scored. We then tested the generality of this across populations: the progress of moult should, therefore, correlate with the average timing of the wet season along a spatial environmental gradient where the rains start at different times each year south-to-north of Nigeria. To test this, we modelled moult progress just before the rains across 15 localities 6°–13° N as a function of the onset of the wet season among localities. As predicted, moult progressed further in localities with earlier wet seasons, confirming that the onset of moult is timed to the onset of the wet season in each locality despite weak breeding seasonality in the Common Bulbul. This strategy may evolve to maintain optimal annual cycle routine in seasonal environments where breeding is prone to unpredictable local perturbations like nest predation. It may, however, be less obvious in temperate systems where all annual cycle stages are seasonally constrained, but it may help with explaining the high frequency of breeding–moult overlaps in tropical birds.</p>
Data for "Resource use divergence facilitates the evolution of secondary syntopy in a continental radiation of songbirds (Meliphagoidea): insights from unbiased co-occurrence analyses"
<p>These two files contain data needed to replicate analyses in the associated article.</p> <p>AUTHOR of data files: Vladimir Remes<br> CONTACT: vlad.remes/at/gmail,com<br> AUTHORS of the article: V. Remes, L. Harmackova<br> DATE CREATED: 8 November 2022<br> ARTICLE: published in Ecography</p> <p> </p> <p>The file named "data_syntopy.xlsx" has two sheets:<br> "data": contains the data<br> "legend": contains explanations of data columns</p> <p>The file was saved in MS Excel for Mac 16.65.</p> <p><br> The file named "tree_Mel.tre" is the phylogenetic tree in the parenthetic format used for the analyses. It has been pruned from the tree published by Marki et al. (2017) Mol Phyl Evol 107, 516–529. It was saved using the write.nexus function from the "ape" package for R software.</p>
Data for: Patterns of extra-territorial nestbox visits in a songbird suggest a role in extra-pair mating
<p class="MsoNormal"><span>Many animals make visits outside of their territory during the breeding period, but these are typically infrequent and difficult to observe. As a consequence, comprehensive data on extra-territorial movements at the population-level are scarce and the function of this behavior remains poorly understood. Using an automated nestbox visit tracking system in a wild blue tit population over six breeding seasons, we recorded all extra-territorial nestbox visits (n=22137) related to 1195 individual breeding attempts (761 unique individuals). Sixty-two percent of breeders made at least one extra-territorial visit between the onset of nest building and the day of fledging of their offspring, and individuals visited another nestbox on average on 11% of the days during this period. Visit behavior differed clearly between the sexes, with males making over three times as many extra-territorial forays as females. There was a strong overall seasonal decline in visit behavior, but this was sex dependent, with females showing a strong reduction in the number of extra-territorial visits before the onset of egg laying and males showing a strong and sudden reduction on the day their offspring hatched. The likelihood of visiting a particular nestbox declined sharply with the distance to that box, and blue tits almost exclusively visited direct neighbors. Individuals were more likely to have extra-pair offspring with an individual whose box they visited, but they were not more likely to disperse to a box they had visited. Thus, our results are inconsistent with the hypothesis that extra-territorial nestbox visits serve to inform dispersal decisions, but suggest that such visits are linked to extra-pair mating opportunities.</span></p>
Migration direction in a songbird explained by two loci
<p><span>Migratory routes and remote wintering quarters in birds are often species and even population specific. It has been known for decades that songbirds mainly migrate solitarily and that the migration direction is genetically controlled. Yet, the underlying genetic mechanisms remain unknown. To investigate the genetic basis of migration direction, we track genotyped willow warblers <em>Phylloscopus</em> <em>trochilus</em> from a migratory divide in Sweden, where South-West migrating and South-East migrating subspecies form a hybrid swarm. We find that migration direction follows a dominant inheritance pattern with epistatic interaction between the two loci explaining 74% of variation. Consequently, most hybrids migrate similarly to one of the parental subspecies and therefore do not suffer from the cost of following an inferior, intermediate route. This has significant implications for understanding the selection processes that maintain narrow migratory divides.</span></p>
Heat tolerance limits of Mediterranean songbirds and their current and future vulnerabilities to temperature extremes
<p>Songbirds are one of the groups most vulnerable to extreme heat events. Although several recent studies have assessed their physiological responses to heat, most of them have focused on arid-zone species solely. We investigated thermoregulatory responses to heat in eight small-sized songbirds occurring in the Mediterranean Basin, where heatwaves are becoming more frequent and intense. Specifically, we determined their heat tolerance limits (HTL) and evaporative cooling efficiency and evaluated their current and future vulnerabilities to heat in southwestern Iberia, a Mediterranean climate warming hotspot. To do this, we exposed birds to an increasing profile of air temperatures (Ta) and measured resting metabolic rate (RMR), evaporative water loss (EWL), evaporative cooling efficiency (the ratio between evaporative heat loss and metabolic heat production) and body temperature (Tb). HTL ranged between 40 and 46°C across species, and all species showed rapid increases in RMR, EWL and Tb in response to increasing Ta. However, only the crested lark Galerida cristata achieved an evaporative cooling efficiency greater than 1. The studied songbirds currently experience summer Ta maxima that surpass their upper critical temperatures of their thermoneutral zone and even their HTL. Our estimates indicated that five of the eight species will experience moderate risk of lethal dehydration by the end of the century. We argue that the limited heat tolerance and evaporative cooling efficiency of small-sized Mediterranean songbirds make them particularly vulnerable to heatwaves, which will be exacerbated under future climate change scenarios.</p>
Local weather and endogenous factors affect the initiation of migration in short- and medium-distance songbird migrants
<p>Migratory birds employ a variety of mechanisms to ensure appropriate timing of migration based on the integration of endogenous and exogenous information. The cues to fatten and depart from the non-breeding area are often linked to exogenous cues such as temperature or precipitation and the endogenous program. Shorter-distance migrants should rely heavily on environmental information when initiating migration given the relatively close proximity to the breeding area. However, the ability to fatten and subsequently depart may be linked to individual circumstances, including current fuel load and body size. For early and late departing migrants, we investigate the effects of temperature, precipitation, lean body mass, fuel load, and day of year on the initiation of migration (i.e., fuel load and departure timing) from the non-breeding region by analyzing 21 years of banding data for four species of short- and medium-distance migrants. Temperatures at the non-breeding area were related to temperatures at potential stopover areas. Despite local cues being predictive of conditions further north, the amount of variation explained by local weather conditions in our models differed by species and temporal period but was low overall (< 33% variation explained). For each species, we also compared lean body mass and fuel load between early and late departing migrants, which showed mixed results. Our combined results suggest that most individuals migrating short or medium distances in our study did not time the initiation of migration with local predictive cues alone, but rather other factors such as lean body mass, fuel load, and day of year, which may be a proxy for the endogenous program, and those beyond the scope of our study also influenced the initiation of migration. Our study contributes to understanding which factors influence departure decisions of short- and medium-distance migrants as they transition from the non-breeding to the migratory phase of the annual cycle.</p>
Virginia marsh songbird rope-drag data – winter 2014
<p class="MsoNormal">Bird species that are restricted to tidal marshes during one or all of their life stages are under increasing pressure from sea-level rise. To date, most of the research focused on this group has been conducted during the breeding season despite the fact that more than half of the annual cycle is spent on wintering grounds and the high likelihood that the winter period is the most critical time for adult survival. We used a double-pass rope-drag technique to estimate the winter abundance of sharp-tailed sparrows (<em>Ammospiza</em> <em>nelson </em>and<em> A. caudacutus</em> collectively), seaside sparrows (<em>A. maritimus</em>) and marsh wrens (<em>Cistothorus palustris</em>) within tidal marshes of Virginia along 102 60×250 m transects between January and March 2014. We used the first pass to remove birds from the transect and the second pass was used to estimate detection probabilities. The technique was highly effective producing detection rates of 98% for sharp-tailed sparrows, 95% for seaside sparrows, and 91% for marsh wrens. We conducted three rounds of surveys and found that species-specific detection rates were comparable when we restricted our analyses to two survey rounds. Availability and abundance estimates deviated to a greater degree than detection rates when restricting data to that collected during only two rounds but confidence intervals overlapped for all three taxa, regardless of which two survey periods were used for the comparison. However, results were less precise when we restricted our analyses to two of three rounds with confidence intervals averaging 13%, 45%, and 14% larger for detection, availability, and abundance respectively. The double-pass rope-drag technique provides an effective, unbiased sampling technique to estimate winter songbird abundance in saltmarsh habitat provided that at least two rounds are used and increasing the number of survey rounds will result in more precise estimates.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.