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Figure 21 in Breeding behavior, distribution, and conservation of the Sharp-tailed Tyrant Culicivora caudacuta (Vieillot, 1818) (Aves: Tyrannidae), a South American grassland specialist
Figure 21. Records of Culicivora caudacuta. Yellow stars indicate museum specimens, dots indicate other categories of records. See Appendix 1 for details.
Figure 22 in Breeding behavior, distribution, and conservation of the Sharp-tailed Tyrant Culicivora caudacuta (Vieillot, 1818) (Aves: Tyrannidae), a South American grassland specialist
Figure 22. Culicivora caudacuta habitat occupation by Eucalyptus sp. monoculture, Araxá, Ribeirão do Inferno (07 May 2014). Photo: RSS.
Figure 1 in Breeding behavior, distribution, and conservation of the Sharp-tailed Tyrant Culicivora caudacuta (Vieillot, 1818) (Aves: Tyrannidae), a South American grassland specialist
Figure 1. Adult Sharp-tailed Tyrant Culicivora caudacuta, (11 October 2011), Patrocínio, Minas Gerais, Brazil. Photo: RSS.
Figure 20 in Breeding behavior, distribution, and conservation of the Sharp-tailed Tyrant Culicivora caudacuta (Vieillot, 1818) (Aves: Tyrannidae), a South American grassland specialist
Figure 20. Specimen of young Culicivora caudacuta at Zoologische Staatssammlung München. Photo: Markus Unsöld.
Data from: Common protein-coding variants and the racing phenotype in galloping racehorse breeds
<p>Centuries-long selection for system-wide morphological, physiological, and metabolic adaptations has led to extreme athletic phenotypes among geographically diverse horse breeds. Here, we identify genes contributing to exercise adaptation in racehorses by applying genomics approaches for racing performance, an end-point athletic phenotype. Using an integrative genomics strategy to first combine population genomics results with skeletal muscle exercise and training transcriptomic data, followed by whole-genome resequencing of Asian horses, we identify protein-coding variants in genes of interest in galloping racehorse breeds (Arabian, Mongolian and Thoroughbred). A core set of genes, <em>G6PC2</em>, <em>HDAC9</em>, <em>KTN1</em>, <em>MYLK2</em>, <em>NTM</em>, <em>SLC16A1</em> and <em>SYNDIG1</em>, with central roles in muscle, metabolism, and neurobiology, are key drivers of the racing phenotype. Although racing potential is a multifactorial trait, the genomic architecture shaping the common athletic phenotype in horse populations bred for racing provides evidence for the influence of protein-coding variants in fundamental exercise-relevant genes. Variation in these genes may therefore be exploited for genetic improvement of horse populations towards specific types of racing.</p>
Replication data for: Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada
<p class="MsoNormal">This data package includes data files and an R script to reproduce results reported in the paper "Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada". Analyses include hierarchical multispecies models applied to data from 31 bird species at 38 Monitoring Avian Productivity and Survivorship (MAPS) stations to assess 10-year (2011–2020) demographic trends and responses to energy sector disturbance (human footprint proportion) in the Athabasca oil sands region of Alberta, Canada. Adult captures, productivity, and residency probability all declined over the study period, and adult apparent survival probability also tended to decline. Trends in adult captures, productivity, and survival were all more negative at stations with larger increases in disturbance over the study period. Species associated with early seral stages were more commonly captured at more disturbed stations, while species typical of mature forests were more commonly captured at less disturbed stations. Productivity was positively correlated with disturbance within 5 km of stations after controlling for disturbance within 1 km of stations. Adult apparent survival showed relatively little response to disturbance; stresses experienced beyond the breeding grounds likely play a larger role in influencing survival. Residency probability was negatively related to disturbance within 1-km scale of stations and could reflect processes affecting the ability of birds to establish or maintain territories in disturbed landscapes.</p>
Brood parasitism risk drives birds to breed near humans
<p>Although humans have generally negative effects on wildlife, some animals live in close proximity to human residences. Why some animals choose to settle near humans remains a long-standing puzzle. Settling near humans or in urban environments may be beneficial, because of the availability of resources such as food (e.g. supplemental feeding) or suitable nest sites (e.g. cavities), or because of reduced predation risk if predators avoid settlements. Here, we report on a study of Daurian redstarts <em>Phoenicurus auroreus</em>, a common host of the common cuckoo <em>Cuculus canorus</em>, to show that settling near humans can also be a strategy employed by hosts to avoid brood parasitism. First, redstarts suffered an increased risk of brood parasitism with increasing distance from the nearest building. Second, redstarts adjusted their nesting location in response to a seasonally predictable change in the risk of brood parasitism. Third, experimentally simulating the presence of cuckoos during a period when they are naturally absent increased the likelihood that redstarts nested indoors or closer to human settlements. These findings suggest that redstarts actively choose to place their nest in the vicinity of a human residence as a defense against cuckoos. Hence, settling near humans may be an anti-parasitism strategy in some avian hosts.</p>
Ruff in breeding plumage
ID no.: MP 047 Museum: The Krystyna and Włodzimierz Tomek Natural Science Museum in Ciężkowice https://muzea.malopolska.pl/en/objects-list/2386 Digitalisation: RDW MIC, Virtual Małopolska project Source: Objaverse 1.0 / Sketchfab
Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
<p><strong>Summary</strong></p> <p>Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for <em>H<sub>O</sub></em> and <em>H<sub>E</sub></em> was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.</p>
Wetland creation and reforestation of legacy surface mines in the Central Applachian Region (USA): A potential climate-adaptation approach for pond-breeding amphibians?
<p>Habitat restoration and creation within human-altered landscapes can buffer the impacts of climate change on wildlife. The Forestry Reclamation Approach (FRA) is a coal surface mine reclamation practice that enhances reforestation through soil decompaction and the planting of native trees. Recently, wetland creation has been coupled with FRA to increase habitat available for wildlife, including amphibians. Our objective was to evaluate the response of pond-breeding amphibians to the FRA by comparing species occupancy, richness, and abundance across two FRA age-classes (2–5-year and 8–1—year reclaimed forests), traditionally reclaimed sites that were left to naturally regenerate after mining, and in mature, unmined forests in the Monongahela National Forest (West Virginia, USA). We found that species richness and occupancy estimates did not differ across treatment types. Spotted Salamanders (<em>Ambystoma maculatum</em>) and Eastern Newts (<em>Notophthalmus viridescens</em>) had the greatest estimated abundances in wetlands in the older FRA treatment. Additionally, larger wetlands had greater abundances of Eastern Newts, Wood Frogs (<em>Lithobates sylvaticus</em>), and Green Frogs (<em>L. clamitans</em>) compared to smaller wetlands. Our results suggest that wetland creation and reforestation increases the number of breeding sites and promotes microhabitat and microclimate conditions that likely maximize the resilience of pond-breeding amphibians to anticipated climate changes in the study area.</p>
Fig. 3 in SHORT COMMUNICATION Monitoring a population of Cruziohyla craspedopus (Funkhouser, 1957) using an artificial breeding habitat
Fig. 3. Newly metamorphosed juvenile Cruziohyla craspedopus.
Data from: Genome-wide scans reveal selection signatures and cross-population variation in South African and European beef cattle breeds
<p>In genetics and evolutionary biology, the concept of selection signatures is used to describe specific patterns in the genome that are associated with the process of natural selection. These selection signatures provide insights into how evolutionary forces have shaped a population over time.In this study, a total of 96 samples were collected in several farms from four different cattle breeds, namely South African indigenous Nguni (n = 28) and Bonsmara (n = 21), Scottish Angus (n = 22), and Swedish Simmental (n = 25). Genotyped samples were subjected to quality control, and a total of 105,675 SNPs from 78 individuals remained for further analysis. Genomic signatures of positive selection within each breed were identified using the Integrated Haplotype Score (iHS) method, and cross-population comparison analysis using cross-population extended haplotype homozygosity ( XP-EHH), relative extended haplotype homozygosity (Rsb), and fixation index (Fst) methods, to assess the genetic differences between breeds. The results from the iHS method revealed selection signatures in two genomic regions for Bonsmara, six for Simmental, four for Nguni, and one for Angus cattle. Ten regions were found to be under selection, with BTA 12 being shared between Nguni and Bonsmara. Comparisons across populations using Rsb, and Fst methods performed better and revealed the most specific genomic regions that varied in selection between breeds. Gene annotation analyses linked candidate genes to several Quantitative Trait Loci (QTL). For example, in Simmental cattle's FAM110B gene was linked to carcass weight and body confirmation score. Bonsmara showed fewer candidate genes, such as CDK8 and FLT1, whereas Angus had none on BTA 18. Nguni identified potential genes such as CRB1, PLAG2GA, and VASH2, with CDK8 shared by Bonsmara and Nguni on BTA 12. Further cross-population studies revealed candidate genes associated with certain traits, genes including as PLCXD3, FAM149B1, and GRIK2 for Bonsmara versus Nguni, and SLIT2 and TSPAN9 for Simmental vs Angus. The study also emphasised gene related to meat quality, reproduction, health, illnesses, fertility, and body conformation score. Gene interaction study with the STRING database revealed a network of 63 candidate genes, demonstrating the structure of genetic connections, some biological processes. The study found that iHS performed well in population analysis with Nguni cattle, having exhibited the highest number of signatures across the genome, and significant signatures were also seen in comparisons between Nguni and Bonsmara using the Fst and Rsb methods. Furthermore, the study discovered that a bigger number of genes were connected with various traits, including sperm count and insemination per conception, sensitivity to bovine respiratory disease, and ease of calving. This genomic analysis underlined the relevance of the genetic relying which distinguishes distinct breeds. This understanding has the potential to significantly enhance selective breeding and increase desirable traits in cattle herds. This genomic analysis underlined the significance of the genetic basis for breed-specific traits. This understanding has the potential to drastically improve selective breeding and increase desirable traits in cattle herds.</p>
Data for: Breeding pairs with color aberrations in Oriental reed warblers
<p>One pair of Oriental red warblers was found with color aberrations. Two videos (ESM Video S1 and Video S2) were provided as supplementary material showing Breeding pairs with color aberrations in Oriental reed warblers. Our study shows that the breeding pair breed normally and further egg experiments indicated they can reject foreign eggs as other breeding pairs.</p>
Data from: Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom
<p><strong>Background: </strong>Sheep breeds native to the United Kingdom are noted for high breed variability and exhibit a striking diversity of different traits in phenotypes and genetic diversity. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including 6 on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.</p> <p><strong>Results: </strong>In this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds.</p> <p><strong>Conclusion: </strong>Our results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small populations sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.</p>
Movements and breeding performance of Bonelli's eagle
<p>Code and data for estimate the relationship between intrinsic (experience) and extrinsic factors (weather), movement behaviours metrics (proportion of time in flight, range of movement and straitghness of trajectories) and breeding performance of Bonelli's eagles <em>Aquila fasciata (French popualtion).</em></p> <p>Mail: <a href="mailto:lise.viollat@protonmail.com">lise.viollat@protonmail.com</a><br>Twitter: @LiseViollat</p> <p><br><strong>Code files </strong></p> <ul> <li>effect_intrinsic_extrinsic_factors_movement_Bonelli: relationships between three movement behaviour metrics (proportion of time in flight, range of movement and straitghness of trajectories) with experience and local weather (rainfall, wind and temperature) in Bonelli's eagle, at a daily scale during the breeding season</li> <li>effect_intrinsic_extrinsic_factors_breeding_Bonelli.Rmd : relationships between breeding performances (breeding probability, hatching success and fledging success) of Bonelli's eagles with recruitment (breeding experience) and weather (rainfall, winf and temperature) during 3 breeding phases (pre-breeding, incubation and rearing).</li> <li>relationship_movement_breeding_Bonelli.Rmd : relationships between the productivity (number of fledging chicks) and movement behaviors metrics (proportion of time in flight, range of movement and straitghness of trajectories) of Bonelli's eagle during 3 breeding phases (pre-breeding, incubation and rearing). </li> </ul>
Movement of juvenile migratory birds from settlement to adulthood across the non-breeding range
<p>Among migratory vertebrates, high levels of fidelity to non-breeding sites during adulthood are common. If occupied sites vary in quality, strong site-fidelity can have profound consequences for individual fitness and population demography. Given the prevalance of adult site-fidelity, the regions of the non-breeding range to which juveniles first migrate, and the scale of any subsequent movements, are likely to be pivotal in shaping distributions and demographic processes across population ranges. However, inherent difficulties in tracking migratory individuals through early life mean that opportunities to quantify juvenile settlement and movements across non-breeding ranges, and the mechanisms involved, are extremely rare.Through long-term, range-wide resightings of hundreds of colour-marked individuals from their first migration to adulthood, and application of state-space models, we quantify levels of juvenile and adult regional-scale movements and distances at different life stages across the whole non-breeding distribution range in a migratory shorebird, the Black-tailed Godwit (<em>Limosa limosa islandica</em>). We show that the probability of individuals changing non-breeding regions (seven historical wintering regions spanning the Western Europe range) at all ages are very low (mean movement probability = 10.9% from first to subsequent winter, and 8.3% from first adult winter to later winters). Movement between regions was also low between autumn and winter of the same year for both juveniles (mean movement probability = 17.0%) and adults (10.4%). The great majority of non-breeding movements from the first autumn to adulthood were within regions and less than 100 km. The scarcity of regional-scale non-breeding movements from the first autumn to adulthood means that the factors influencing where juveniles settle will be key determinants of non-breeding distributions and of the rate and direction of changes in distributions.</p>
Figure 1 in Non-breeding season records of the Alpine Leaf Warbler Phylloscopus occisinensis
Figure 1. Sampling localities of Phylloscopus affinis (sensu lato) in Bangladesh and Thailand.
Fig 8 in Culture and breeding of Ompok bimaculatus, Pabda (Indian Butter catfish), seed production in North-East, India
Fig 8: Feeding of larvae
Fig 7 in Culture and breeding of Ompok bimaculatus, Pabda (Indian Butter catfish), seed production in North-East, India
Fig 7: Hormonal breeding
Fig 6 in Culture and breeding of Ompok bimaculatus, Pabda (Indian Butter catfish), seed production in North-East, India
Fig 6: Broodstock tank
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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.