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FIGURE 9 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 9. The type of M. melanocephalus malaris Zimmer, 1949 (AMNH 235067). Dorsal, ventral, and side views, with the detail of the face. Currently treated as a subspecies of a Myioborus melanocephalus. Photographs by Paul Sweet (American Museum of Natural History).
FIGURE 3 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 3. Top: the syntype of Setophaga bairdi Salvin, 1878 (NHMUK 1885.3.8.801). This specimen exhibits the facial color and pattern observed in individuals from most of the Ecuadorian Andes that are currently considered as the "pure" southern form hybridizing with chrysops (Céspedes-Arias et al. 2021). Photographs by Mark Adams (Natural History Museum, Tring). Bottom: the type of Myioborus bairdi griseonuchus Chapman, 1927 (AMNH 229332). This taxon is restricted to northern Peru (departments of Piura and Cajamarca). Photographs by Paul Sweet (American Museum of Natural History).
FIGURE 2 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 2. Photographs of the type specimen of Setophaga ruficoronata Kaup, 1851 (NML-VZ D1931) currently treated as Myioborus melanocephalus ruficoronatus. Side and dorsal views, with the detail of the front and face, and its label. The type exhibits intermediate facial color and pattern as observed in the center of the hybrid zone near Pasto, Department of Nariño, southern Colombia (Céspedes-Arias et al. 2021). Photographs by Tony Parker and John James Wilson (World Museum, National Museums Liverpool).
FIGURE 1 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 1. Map of northwestern South America showing the geographic distribution of high-elevation Myioborus warblers of the Northern Andes (M. albifrons, M. ornatus and M. melanocephalus). Each colored polygon represents the approximate geographic distribution of taxa recognized in this study, except for the one in dark gray, which shows the extent of the hybrid zone (Céspedes-Arias et al. 2021) between chrysops and bairdi. Gray dots indicate type localities of valid taxa, and the star the location of Cali, Colombia, the supposed type locality of M. m. ruficoronatus, which is most likely an error (see text). The question mark indicates the uncertainty in the geographic limits between bairdi and griseonuchus in southern Ecuador.
FIGURE 7 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 7. The type of Setophaga chrysops Salvin, 1878 (NHMUK 1885.3.8.804). Dorsal, ventral and side views, with the detail of the face. This taxon is currently treated as M. ornatus chrysops, and is the "pure" northern form hybridizing with bairdi in southern Colombia (see text). Photographs by Mark Adams (Natural History Museum, Tring).
FIGURE 6 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 6. Type specimens of names synonymized with Myioborus ornatus sensu stricto, and M. chrysops. Types of flaveola (A, MCZ 76106) and leucophomma (B, NML-VZ D2009), which correspond to juvenile and immature individuals of M. ornatus, respectively. Kaup (1851) identified as flaveola a specimen that corresponds to M. chrysops (C, NML-VZ D1932), but this is not a true type specimen (see text). Photographs by Jeremiah Trimble (Museum Comparative Zoology, Harvard University), and by Tony Parker and John James Wilson (World Museum, National Museums Liverpool).
FIGURE 5 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 5. Type of Setophaga ornata Boissonneau, 1840 (MCZ 76106), currently treated as Myioborus ornatus sensu stricto. Dorsal, ventral, and side views, with the detail of the face. This is a "Bogotá" skin. Photographs by Jeremiah Trimble (Museum Comparative Zoology, Harvard University).
FIGURE 4 in The type of Setophaga ruficoronata (Kaup 1851) is a hybrid: implications for the taxonomy of Myioborus warblers (Passeriformes: Parulidae)
FIGURE 4. Illustrations of three Andean Myioborus as illustrated by Johannes Gerardus Keulemans in Salvin (1878). Top: chrysops of the Western and Central cordilleras of Colombia. Center: A hybrid individual painted based on the type of Setophaga ruficoronata (NML-VZ D1931, see Fig. 2). Bottom: bairdi based on a specimen assigned to Setopopha bairdi from Sical (sic) Ecuador (see Fig. 3). The taxon bairdi was until now considered a junior synonym of ruficoronatus (Meyer de Schauensee 1946). Illustrations from Salvin (1878) via the Biodiversity Heritage Library (https://www.biodiversitylibrary.org/item/34861)
Genotype likelihoods for low-coverage whole-genome sequencing data of yellow warblers
<p>The following datasets include the required input files used to empirically test population assignment in WGSassign on Yellow Warbler data. The file "yewa.known.ind105.ds_2x.beagle.gz" includes the filtered variants of 105 Yellow Warbler individuals output as genotype likelihoods and stored in a Beagle-formatted file. The ID file, "yewa.known.ind105.reference.IDs.txt", is a tab-delimited file with 2 columns, the first being the sample ID, and the second being the known reference population. The sample order in the ID file should match that of the input beagle file. To measure the assignment accuracy of WGSassign, we used leave-one-out cross validation using the input beagle file and our ID file.</p>
Data from: Catastrophic storms, forest disturbance, and the natural history of Swainson's warbler
<p>The core breeding range of Swainson's warbler (<em>Limnothlypis swainsonii</em>) overlaps a zone of exceptionally high tornado frequency in southeastern North America. The importance of tornadoes in creating breeding habitat for this globally rare warbler and other disturbance-dependent species has been largely overlooked. This paper estimates tornado frequency (1950–2021) and forest disturbance in the 240 counties and parishes in which breeding was documented from 1988 to 2014. The frequency of destructive tornadoes (EF1-EF5) varied 6-fold across the breeding range with a peak in the Gulf Coast states. Counties from east Texas to Alabama experienced the lowest median return interval of 5.4 years per 1000 km<sup>2</sup>, resulting in approximately 2477 ha of forest damage per 1000 km<sup>2</sup> per century, based on current forestland cover. Tornadoes were significantly less frequent north and east of the core breeding range, with return intervals increasing to 9.1 years per 1000 km<sup>2</sup> for breeding counties on the Atlantic coastal plain, 10.2 years per 1000 km<sup>2</sup> in the Ozark Mountains, and 32.3 years per 1000 km<sup>2</sup> in the Appalachian Mountains. Breeding counties within 150 km of the coastline from east Texas to North Carolina are also subjected to the highest frequency of hurricanes in the Western Hemisphere. Hurricanes often cause massive forest damage but archived meteorological and forestry data are insufficient to estimate the aggregate extent of forest disturbance in breeding counties. Nevertheless, the combined impact of tornadoes and hurricanes in the pre-Anthropogenic era was likely sufficient to produce a dynamic mosaic of early-successional forest crucial for the breeding ecology of Swainson's warbler. To ensure the long-term survival of this rare warbler, it is advisable to develop habitat management plans that incorporate remote sensing data on early-successional forest generated by catastrophic storms as well as anthropogenic activities.</p> <p>This dataset comprises a catalog of 1717 song recordings of male Swainson's warblers (<em>Limnothlypis swainsonii</em>) on breeding territories in the southeastern United States. Songs were recorded from 1988 to 2014. The spreadsheet includes song recording field number (GRG), state, county or parish, date, latitude, and longitude. Breeding territories were located in 240 counties and parishes, which served as the geographic template for storm data analysis. Geographic coordinates were plotted in Fig 1 of "Catastrophic storms, forest disturbance, and the natural history of Swainson's warbler" (doi.org/10.1002/ece3.11099). Questions or inquiries regarding the dataset can be directed to the author. </p>
Dataset on the content of Cu, Ni Cd, Pb, Zn, Ag, Mg, Fe, Co and Ca in the carcass, gastrointestinal tract tissues and the whole body of nestlings of a small passerine bird, the Eurasian Reed Warbler Acrocephalus scirpaceus
<p><span>The data include the description of the age and the </span><span>concentrations of </span><span>Cu, Ni Cd, Pb, Zn, Ag, Mg, Fe, Co and Ca<span> measured in the </span>isolated, emptied gastrointestinal tract, <span>the whole body, and </span>carcass of the each individual nestling of a different age and hence a different stage of <span>post-natal development. The dataset includes also</span> some additional information on the breeding biology of the focal species. </span></p>
Complex post-breeding moult strategies in a songbird migrating along the East Asian flyway, the Pallas's Grasshopper Warbler Locustella certhiola
<p>Moult strategies have received relatively little attention in current ornithology, and knowledge concerning the evolution, variability, and extent of moult is sparse in many bird species. This is especially true for East Asian <em>Locustella</em> species where assumptions on moult patterns are based on incomplete information. We provide evidence indicating a complex post-breeding moult strategy and variable moult extent among Pallas's Grasshopper Warbler <em>Locustella certhiola</em>, based on data from six ringing sites situated along its flyway from the breeding grounds to the wintering areas. A detailed study revealed for the first time that in most individuals wing feather moult proceeds from the centre both towards the body and the wing-tip, a moult pattern known as partial divergent moult (which is rare among Palaearctic passerines). In the Russian Far East, where both breeding birds and passage migrants occur, a third of the adult birds were moulting in late summer. In Central Siberia, at the northwestern limit of its distribution, adult individuals commenced their primary moult partly divergently and partly with unknown sequence. During migration in Mongolia, only descendantly (i.e. from the body towards the wing-tip) moulting birds were observed, while further south in Korea, Hong Kong and Thailand the proportion of potential eccentric and divergent feather renewal was not identifiable since the renewed feathers were already fully grown as expected. We found an increase in the mean number of moulted primaries during the progress of the autumn migration. Moderate body mass levels and low fat and muscle scores were observed in moulting adult birds, without any remarkable increase in the later season. According to optimality models, we suggest that an extremely short season of high food abundance in tall grass habitats and a largely overland route allow autumn migration with low fuel loads combined with moult-migration in at least a part of the population. This study highlights the importance of further studying moult strategy as well as stopover behaviour decisions and the trade-offs among migratory birds that are now facing a panoply of anthropogenic threats along their flyways.</p>
Data from: Individual and sex-related patterns of prolonged flights during both day and night by great reed warblers crossing the Mediterranean Sea and Sahara Desert
<p>A wide variety of the barrier crossing strategies exist among migrating songbirds, ranging from strict nocturnal flights to non-stop flights over a few days. We evaluate barrier crossing strategies in a nocturnally migrating songbird crossing the Mediterranean Sea and the Sahara Desert, the great reed warbler, exploring variation between the sexes and within individuals. We used data from 31 year-round light-level geolocators tracks from 26 individuals (13 males and 13 females), with four individuals tracked for 2–3.5 consecutive years. Almost all individuals (25 of 26) prolonged their flights into the day at least on one occasion. The mean duration of these prolonged flights was 19.9 h and did not differ between sexes or seasons. Fifteen birds performed non-stop flights during more than one full day and night (≥ 24 h; mean = 31.9 h; max = 55 h) in autumn and/ or spring, but these flights were generally too short to cross an entire barrier (such as the Sahara Desert) in one non-stop flight. Patterns of prolonged flights showed considerable within-individual variation in females between seasons (autumn versus spring) and in both males and females between years, suggesting high individual flexibility in migration strategy. Significantly more males than females performed prolonged flights during autumn migration, but not spring, possibly reflecting sex-specific carry-over effects. We conclude that great reed warblers have the ability to conduct prolonged continuous flights for up to several nights and days, which potentially would allow them to cross the Sahara Desert in one non-stop flight. However, they typically use a mixed strategy of several nocturnal flights with intermittent stopovers in combination with 1–3 prolonged flights. Prolonged flights covered less than half (44%) of the total flight time across the barriers, and the diurnal parts of the flights covered only 18% of this time.</p>
Fig. 2 Minimum-spanning network among 44 in Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the Marsh Warbler Acrocephalus palustris (Aves: Acrocephalidae)
Fig. 2 Minimum-spanning network among 44 COI haplotypes of Marsh Warbler (see Table S2). Size of circles represents the relative frequency of given haplotypes and each line between black nodes indicates a single mutational step
Fig. 3 in Mitochondrial evidence for genetic diversity and low phylogeographic differentiation in the Marsh Warbler Acrocephalus palustris (Aves: Acrocephalidae)
Fig. 3 Left: Mismatch distribution. Expected (solid line) and observed (broken line) mismatch distribution under population expansion model. Right: Bayesian skyline plot representing the historical demographic
Fig. 1 in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)
Fig. 1 Distributional limits of Sericornis and Crateroscelis in the Australo-Papuan region. Distribution of the Australo-Papuan-centred group is shown in the main figure. The white-browed scrubwren (S. frontalis) complex has the broadest distribution in Australia (stippled area) and is divided into an eastern frontalis and western maculatus group. The remaining Australian scrubwrens are restricted to the east
Fig. 6 in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)
Fig. 6 Biogeographic reconstruction showing possible routes of dispersal as a function of asynchronous Central Range orogeny and eustatic falls in sea level. a Initial colonisation of western New Guinea during the late Miocene after the onset of orogeny in western new Guinea ~ 12 Mya. Colonisation from northern Australian mesic forests is inferred to have occurred during periods of lowered sea level when a deltaic environment, formed by the accumulation of shedding siliclastics, developed on the Arafura shelf. b Pliocene diversification of New Guinean sericornithinines coincides with a phase or rapid mountain uplift and suggests passive transport of species to higher elevations. c Pleistocene connectivity across the Torres Strait in the magnirostra group coincident with periods of lower sea level during glacial maxima. Dispersal across the Arafura shelf is unlikely at this time due to the contraction of mesic
Fig. 4 in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)
Fig. 4 Maximum clade credibility tree for the Sericornithinae generated in BEAST using a strict molecular clock and Yule speciation prior. Species names for scrubwrens and mouse-warblers are in black type with altitudinal replacement sequences in shaded boxes. Alternative placement of S. citreogularis supported by Bayesian hypothesis testing is indicated by the dashed arrow linking branches. Mean node ages (Mya) are shown
Fig. 5 3D in Ecological and evolutionary diversification in the Australo-Papuan scrubwrens (Sericornis) and mouse-warblers (Crateroscelis), with a revision of the subfamily Sericornithinae (Aves: Passeriformes: Acanthizidae)
Fig. 5 3D plot of principal components of ecomorphological divergence in New Guinean Sericornis and Crateroscelis. Letters A–D denote the four altitudinal replacement sequences recovered in the phylogenetic tree (Fig. 4). The figure was prepared in scatterplot3D and Adobe Illustrator CS6 (colour available online)
Data from: Oxidative status and fitness components in the Seychelles warbler
Oxidative damage, caused by reactive oxygen species during aerobic respiration, is thought to be an important mediator of life-history trade-offs. To mitigate oxidative damage, antioxidant defence mechanisms are deployed, often at the cost of resource allocation to other body functions. Both reduced resource allocation to body functions and direct oxidative damage may decrease individual fitness, through reducing survival and/or reproductive output. The oxidative costs of reproduction have gained much attention recently, but few studies have investigated the long-term consequences of oxidative damage on survival and (future) reproductive output under natural conditions. Using a wild population of the cooperatively breeding Seychelles warbler (Acrocephalus sechellensis), we tested the prediction that high levels of reactive oxygen species, or high antioxidant investments to avoid oxidative damage, have fitness consequences because they reduce survival and/or reproductive output. We found that individuals with higher circulating non-enzymatic antioxidant capacity had a lower probability of surviving until the next year. However, neither current reproductive output, nor future reproductive output in the surviving individuals, was associated with circulating non-enzymatic antioxidant capacity or oxidative damage. The negative relationship between antioxidant capacity and survival that we observed concurs with the findings of an extensive comparative study on birds, however the mechanisms underlying this association remain to be resolved.
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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.