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Figure 3 in New distribution and breeding record of Wroughton's free-tailed bat (Otomops wroughtoni) (Chiroptera: Molossidae) from Meghalaya, India
Figure 3: The mating of Otomops wroughtoni observed in the cave at Pynurkba village in East Jaintia Hills, Meghalaya, India.
Figure 2 in New distribution and breeding record of Wroughton's free-tailed bat (Otomops wroughtoni) (Chiroptera: Molossidae) from Meghalaya, India
Figure 2: The roost locations of Otomops wroughtoni in Meghalaya (4 known, 1 new) and Karnataka (1 known), India.
Table ¹: Consolidated list of known roost locations of Otomops wroughtoni. in New distribution and breeding record of Wroughton's free-tailed bat (Otomops wroughtoni) (Chiroptera: Molossidae) from Meghalaya, India
<p><b>Table ¹:</b> Consolidated list of known roost locations of <i>Otomops wroughtoni.</i></p><table><tbody><tr><th><b>Sl. no.</b></th><th><b>Location name</b></th><th><b>District</b></th><th><b>Country</b></th><th><b>Coordinates</b></th><th><b>Source</b></th></tr></tbody><tbody><tr><th>1</th><td>Pynurkba</td><td>Jaintia Hills</td><td>India</td><td>25°15′ N, 92°17′ E</td><td>Ruedi et al. (2014), present study</td></tr><tr><th>2</th><td>Umlatdoh</td><td>Jaintia Hills</td><td>India</td><td>25°12′ N, 92°16′ E</td><td>Ruedi et al. (2014)</td></tr><tr><th>3</th><td>Thangsah</td><td>Jaintia Hills</td><td>India</td><td>25°11′ N, 92°12′ E</td><td>Ruedi et al. (2014)</td></tr><tr><th>4</th><td>Shella confederacy</td><td>East Khasi Hills</td><td>India</td><td>25°11′ N, 91°37′E</td><td>Thabah and Bates (2002)</td></tr><tr><th>5</th><td>Mikadogre</td><td>South Garo Hills</td><td>India</td><td>25°23′ N, 90°18′ E</td><td>Present study</td></tr><tr><th>6</th><td>Bhimgad Wildlife Sanctuary</td><td>Belgaum</td><td>India</td><td>15°33′ N, 74°19′ E</td><td>Bates and Harrison (1997)</td></tr><tr><th>7</th><td>Chhep District</td><td>Chhep District</td><td>Cambodia</td><td>13°45′ N, 105°23′ E</td><td>Walston and Bates (2001)</td></tr></tbody></table>
Data from: Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony
Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence. In this study, we performed an ancient DNA analysis of scarlet macaws recovered from archaeological sites in Chaco Canyon and the contemporaneous Mimbres area of New Mexico. All samples were directly radiocarbon dated between 900 and 1200 CE. We reconstructed complete or near-complete mitochondrial genome sequences of 14 scarlet macaws from five different sites. We observed remarkably low genetic diversity in this sample, consistent with breeding of a small founder population translocated outside their natural range. Phylogeographic comparisons of our ancient DNA mitogenomes with mitochondrial sequences from macaws collected during the last 200 years from their endemic Neotropical range identified genetic affinity between the ancient macaws and a single rare haplogroup (Haplo6) observed only among wild macaws in Mexico and northern Guatemala. Our results suggest that people at an undiscovered pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the SW.
Data from: A significant component of ageing (DNA damage) is reflected in fading breeding colors: an experimental test using innate antioxidant mimetics in painted dragon lizards
A decade ahead of their time, von Schantz and coworkers united sexual selection and free radical biology by identifying causal links between deep-rooted physiological processes that dictate resistance to toxic waste from oxidative metabolism (reactive oxygen species), and phenotypic traits, such as ornaments. Ten years later, these ideas have still only been tested with indirect estimates of free radical levels (oxidative stress) subsequent to the action of innate and dietary antioxidants. Here we measure net superoxide (a selection pressure for antioxidant production) and experimentally manipulate superoxide antioxidation using a synthetic mimetic of superoxide dismutase, Eukarion 134 (EUK). We then measure the toxic effect of superoxide in terms of DNA erosion and concomitant loss of male breeding coloration in the lizard, Ctenophorus pictus. Control males suffered more DNA damage than EUK-males. Spectroradiometry showed that male coloration is lost in relation to superoxide and covaries with DNA erosion; in control males these variables explained 72 % of color loss, whereas in EUK males, the fading of coloration was unaffected by superoxide and unrelated to DNA damage. Thus, EUK's powerful antioxidation removes the erosion effect of superoxide on coloration and experimentally verifies the prediction that colors reflect innate capacity for antioxidation.
Data from: Widespread introgression in Chinese indigenous chicken breeds from commercial broiler
Chinese indigenous chickens constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality, and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on Chinese indigenous chickens. Using the chicken 60K single-nucleotide polymorphism (SNP) chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations, and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all Chinese indigenous chickens. Approximately 15% of the genome, on average, of Chinese indigenous chickens was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to Chinese indigenous chickens at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of Chinese indigenous chickens.
Data from: Sex-specific prey partitioning in breeding piscivorous birds examined via a novel, non-invasive approach
Piscivorous birds frequently display sex-specific differences in their hunting and feeding behaviour, which lead to diverging impacts on prey populations. Cormorants (Phalacrocoracidae), for example, were previously studied to examine dietary differences between the sexes and males were found to consume larger fish in coastal areas during autumn and winter. However, information on prey partitioning during breeding and generally on sex-specific foraging in inland waters is missing. Here, we assess sex-specific prey choice of Great Cormorants (Phalacrocorax carbo) during two subsequent breeding seasons in the Central European Alpine foreland, an area characterized by numerous stagnant and flowing waters in close proximity to each other. We developed a unique, non-invasive approach and applied it to regurgitated pellets: molecular cormorant sexing combined with molecular fish identification and fish-length regression analysis performed on prey hard parts. Altogether, 364 pellets delivered information on both, bird sex and consumed prey. The sexes differed significantly in their overall prey composition, even though Perca fluviatilis, Rutilus rutilus and Coregonus spp. represented the main food source for both. Albeit prey composition did not indicate the use of different water bodies by the sexes, male diet was characterized by higher prey diversity within a pellet and the consumption of larger fish. The current findings show that female and male cormorants to some extent target the available prey spectrum at different levels. Finally, the comprehensive and non-invasive approach has great potential for application in studies of other piscivorous bird species.
Data from: Comparing measures of breeding inequality and opportunity for selection with sexual selection on a quantitative character in bighorn rams
The reliability and consistency of the many measures proposed to quantify sexual selection have been questioned for decades. Realized selection on quantitative characters measured by the selection differential i was approximated by metrics based on variance in breeding success, using either the opportunity for sexual selection Is or indices of inequality. There is no consensus about which metric best approximates realized selection on sexual characters. Recently, the opportunity for selection on character mean OSM was proposed to quantify the maximum potential selection on characters. Using 21 years of data on bighorn sheep (Ovis canadensis), we investigated the correlations between seven indices of inequality, Is, OSM and i on horn length of males. Bighorn sheep are ideal for this comparison because they are highly polygynous, sexually dimorphic, ram horn length is under strong sexual selection, and we have detailed knowledge of individual breeding success. Different metrics provided conflicting information, potentially leading to spurious conclusions about selection patterns. Iδ, an index of breeding inequality, and to a lesser extent Is, showed the highest correlation with i on horn length, suggesting that these indices document breeding inequality in a selection context. OSM on horn length was strongly correlated with i, Is, and indices of inequality. By integrating information on both realized sexual selection and breeding inequality, OSM appeared to be the best proxy of sexual selection and may be best suited to explore its ecological bases.
Data from: Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird
Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick-billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick-billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome-wide markers mapped to a newly assembled thick-billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non-breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.
Data from: Impact of urbanization on abundance and phenology of caterpillars and consequences for breeding in an insectivorous bird
Urbanization can have marked effects on plant and animal populations' phenology, population size, predator-prey interactions and reproductive success. These aspects are rarely studied simultaneously in a single system, and some are rarely investigated, e.g. how insect phenology responds to urban development. Here, we study a tri-trophic system of trees – phytophagous insects (caterpillars) – insectivorous birds (great tits) to assess how urbanization influences i) the phenology of each component of this system, ii) insect abundance and iii) avian reproductive success. We use data from two urban and two forest sites in Hungary, central Europe, collected over four consecutive years. Despite a trend of earlier leaf emergence in urban sites there is no evidence for an earlier peak in caterpillar abundance. Thus, contrary to the frequently stated prediction in the literature, the earlier breeding of urban bird populations is not associated with an earlier peak in caterpillar availability. Despite this the seasonal dynamics of caterpillar biomass exhibited striking differences between habitat types with a single clear peak in forests, and several much smaller peaks in urban sites. Caterpillar biomass was higher in forests than urban areas across the entire sampling period, and between 8.5 and 24 times higher during the first brood's chick-rearing period. This higher biomass was not associated with taller trees in forest sites, or with tree species identity, and occurred despite most of our focal trees being native to the study area. Urban great tits laid smaller clutches, experienced more frequent nestling mortality from starvation, reared fewer offspring to fledging age, and their fledglings had lower body mass. Our study strongly indicates that food limitation is responsible for lower avian reproductive success in cities, which is driven by reduced availability of the preferred nestling diet, i.e. caterpillars, rather than phenological shifts in the timing of peak food availability.
Data from: Experimentally provided conspecific cues boost bird territory density but not breeding performance
Decision-making during different life-history stages requires information, which is obtained through own or others' experience and interaction with the environment. In birds, song is important for territory defense and mate attraction. Although song has evolved to purposely convey information, it can be inadvertently exploited by conspecifics. Experiments attempting to attract focal species by playing back their song are numerous, yet the consequences for reproductive performance remain little understood. In 2013 and 2014, settlement, reproduction, and extrapair paternity of Phylloscopus sibilatrix were assessed in a randomized experiment. We hypothesized that territory number, reproductive performance, and extrapair paternity would be higher on song plots (wood warbler song playbacks during prebreeding periods) than on control plots (no wood warbler song playback). On song plots, 3 times more territories were established, settlement occurred faster, and maximum plot occupancy was higher compared with control plots. Pairing rate, daily nest survival rate, mean clutch size, mean number of nestlings and fledglings, rates of extrapair young, nest abandonment, and nest predation did not differ between treatments, but fledging success was lower on song plots compared with control plots. This study shows the important role social cues can play for territory selection of birds, but also exemplifies the necessity for postattraction evaluation of reproduction to rule out negative effects of artificial attraction. Decreased fledging success on song plots and ambiguity about consequences of artificial attraction for distribution and settling dynamics of the species give reason to further evaluate whether acoustic attraction represents a suitable method for songbird conservation.
Data from: Non-breeding range size predicts the magnitude of population trends in trans-Saharan migratory passerine birds
Understanding why populations of some migratory species show a directional change over time, i.e. increase or decrease, while others do not, remains a challenge for ecological research. One possible explanation is that species with smaller non-breeding ranges may have more pronounced directional population trends, and their populations are thus more sensitive to the variation in environmental conditions in their non-breeding quarters. According to the serial residency hypothesis, this sensitivity should lead to higher magnitudes (i.e. absolute values) of population trends for species with smaller non-breeding ranges, with the direction of trend being either positive or negative depending on the nature of the environmental change. We tested this hypothesis using population trends over 2001–2012 for 36 sub-Saharan migratory passerine birds breeding in Europe. Namely, we related the magnitude of the species' population trends to the size of their sub-Saharan non-breeding grounds, whilst controlling for factors including number of migration routes, non-breeding habitat niche and wetness, breeding habitat type and life-history strategy. The magnitude of species' population trends grew with decreasing absolute size of sub-Saharan non-breeding ranges, and this result remained significant when non-breeding range size was expressed relative to the size of the breeding range. After repeating the analysis with the trend direction, the relationship with the non-breeding range size disappeared, indicating that both population decreases and increases are frequent amongst species with small non-breeding range sizes. Therefore, species with small non-breeding ranges are at a higher risk of population decline due to adverse factors such as habitat loss or climatic extremes, but their populations are also more likely to increase when suitable conditions appear. As non-breeding ranges may originate from stochasticity of non-breeding site selection in naive birds ('serial-residency' hypothesis), it is crucial to maintain a network of stable and resilient habitats over large areas of birds' non-breeding quarters.
Age-related breeding success in little penguins: A result of selection and ontogenetic changes in foraging and phenology
<p>Reproductive performance typically improves with age, reaching a plateau at middle age and subsequently declining in older age classes (senescing individuals). Three potential non-exclusive mechanisms can explain the improvement in reproductive performance with age: (1) selection (poor quality individuals are removed from the population with increasing age), (2) constraint (individual efficiency increases through experience) and (3) restraint (reproductive investment increases with age as the residual reproductive value decreases). While all three mechanisms received strong empirical support, few studies have aimed at teasing apart those hypotheses and understanding their underlying functioning. In little penguins (Eudyptula minor), we used a 19-year longitudinal dataset on breeding and foraging of more than 450 individuals to investigate the effect of age on breeding success. We separated within- from among-individual age-effects using state-of-the-art statistical methods (within-subject centering and population change decomposition). We then assessed whether within-individual changes in breeding resulted from ontogenetic changes in foraging performances, breeding phenology or access to mates and nest sites. Fidelity and assortative pairing explained the high correlation in male and female ages within a pair. Breeding performances followed a typical bell-shaped curve with performance increasing up to 8 years-old, before reaching a plateau and subsequently declining after age 16. Both selection and within-individual processes occurred, although within-individual changes dominated differences in age-dependent breeding success. The selective appearance had almost no effect (apart from ages 2 to 3), and selective disappearance mostly affected changes at old ages (above 16), although they were also responsible for the slight increase in reproductive performances from ages 5 to 8. Focusing on within-individual changes, birds exhibited higher performances at middle ages, with birds foraging better, laying earlier and changing partner and nest less often. Their reproductive investment did not vary with age for females and slightly decreased for males. This supports the constraint hypothesis but not the restraint one. Finally, the increase in breeding performances at young ages was explained by the age-related increase in foraging performances during chick-rearing and advancement of laying. In contrast, reproductive senescence was defined by a general decrease in bird performances.</p>
Figure 2 in Breeding biology of a high altitudinal Aethopyga sunbird in southwestern China
Figure 2. The sexual differences of parents on feeding frequencies in three nests of the Fire-tailed Sunbird. Feeding frequency was calculated as the number of feeding bouts per hour made by males and females during each successive observation in each nest. The error bars represent the confidence intervals of feeding frequencies of males and females within each nest.
Figure 3 in Breeding biology of a high altitudinal Aethopyga sunbird in southwestern China
Figure 3. The morphological developments of the nestlings of the Fire-tailed Sunbird. Six morphological traits were included. Body mass was measured in g, and other measurements (lengths of body, bill, tail, tarsus, and wing) were measured in cm. Note that the sample sizes of nestlings measured are not the same in different periods, as some nestlings were depredated or found after being hatched.
Figure 1 in Breeding biology of a high altitudinal Aethopyga sunbird in southwestern China
Figure 1. The nest with two nestlings (a), eggs (b), and predator (the Spotted Nutcracker) (c) of the Fire-tailed Sunbird in southwestern China.
Figure 2 in Territorial behaviour and breeding in the Southern Antpipit Corythopis delalandi (Aves: Rhynchocyclidae) in southeastern Brazil
Figure 2. Nests and eggs of the Southern Antpipit Corythopis delalandi found in fragments of semideciduous forest in Minas Gerais, southeastern Brazil. (a) Female incubating at her nest in Viçosa in November 1993. (b) Nest with two eggs found in Ipoema in 11th of November 2017. (c) Nest under construction found in Florestal in 6th of October 2017. (d) The two eggs clutch from the Ipoema nest.
Early social deprivation shapes neuronal programming of the social decision-making network in a cooperatively breeding fish
The early social environment an animal experiences may have pervasive effects on its behaviour. The Social Decision-Making network (SDMN), consisting of interconnected brain nuclei from the forebrain and midbrain, is involved in the regulation of behaviours during social interactions. In species with advanced sociality such as cooperative breeders, offspring are exposed to a large number and a great diversity of social interactions every day of their early life, which may have life-long consequences on the development of several neurophysiological systems within the SDMN, although these effects are largely unknown. We studied these life-long effects in a cooperatively breeding fish, Neolamprologus pulcher, focusing on the expression in the SDMN of genes involved in the monoaminergic and stress response systems. N. pulcher fry were raised until an age of two months either with their parents, subordinate helpers and same clutch siblings (+F), or with same clutch siblings only (-F). Analysis of the expression of glucocorticoid receptor (GR), mineralcorticoid receptors (MR), corticotropin releasing factor (CRF), dopamine receptors 1 and 2, serotonin transporter (SERT) and DNA methyltransferase I (DNMT1) genes showed that early social experiences altered the neurogenomic state of the preoptic area (POA) of the hypothalamus. The dopamine receptor 1 gene was up-regulated in the POA of -F fish, compared to +F fish. -F fish also showed up-regulation of GR1 expression in the dorsal medial telencephalon (homologous to the basolateral amygdala). Our results suggest that early social environment has life-long effects on the development of several neurophysiological systems within the SDMN. --
Figure 1 in Territorial behaviour and breeding in the Southern Antpipit Corythopis delalandi (Aves: Rhynchocyclidae) in southeastern Brazil
Figure 1. Home ranges of nine males of the Southern Antpipit Corythopis delalandi monitored in a fragment of a secondary semideciduous forest in the municipality of Florestal, Minas Gerais, southeastern Brazil. Two polygons are shown for each bird. The outer polygon was built using a Kernel Density Estimator (KDE), while the inner was built using the Minimum Convex Polygon (MCP). Polygons are numbered as in Table 1. Each symbol represents a location recorded with a GPS handheld device. Note some few cases of intrusions in the home range of neighbour males.
Figure 3 in Territorial behaviour and breeding in the Southern Antpipit Corythopis delalandi (Aves: Rhynchocyclidae) in southeastern Brazil
Figure 3. Number of breeding records of the Southern Antpipit Corythopis delalandi obtained throughout its range. Records include breeding condition birds with enlarged testes, nests being built, nests with eggs, nests with nestlings, and juveniles. Data are from our own fieldwork, literature revision, and Citizen Science Networks (see main text for additional information).
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.