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34 results for “local breeds”
Data archive for "Flight behaviour of Red Kites within their breeding area in relation to local weather variables: Conclusions with regard to wind turbine collision mitigation"
<p>The archive contains the data files to reproduce the results presented in the article “Flight behaviour of Red Kites within their breeding area in relation to local weather variables: Conclusions with regard to wind turbine collision mitigation” published in the Journal of Applied Ecology.</p>
Supplementary material 1 from: Pontoppidan M, Nachman G (2013) Changes in behavioural responses to infrastructure affect local and regional connectivity – a simulation study on pond breeding amphibians. Nature Conservation 5: 13-28. https://doi.org/10.3897/natureconservation.5.4611
Full model description following the ODD-template suggested by Grimm et al. (2006, 2010) and model parameterisation. (doi: 10.3897/natureconservation.5.4611.app). File format: Adobe PDF document (pdf).:
Figure 5 in Effect of season and housing systems on various physiobehavioral attributes of local breed of rabbits (Oryctolagus cuniculus) in Southern Punjab, Pakistan
Figure 5. Effect of seasons on TSL of male rabbits under cage system. Data is mean (± SE) and different letters on the bars depict statistical difference at (p ≤ 0.05) for seasons.
Figure 4 in Effect of season and housing systems on various physiobehavioral attributes of local breed of rabbits (Oryctolagus cuniculus) in Southern Punjab, Pakistan
Figure 4. Effect of housing system on various physiological attributes of rabbits. Data is mean (± SE). Similar letters on the bars indicate non-significant (p ≥ 0.05) difference within caged and colony reared rabbits for rectal temperature. Different letters on the bars indicate significant (p ≤ 0.05) difference within caged and colony reared rabbits for respiration rate.
A Survey of Pathogens on Lamb Carcasses from Portuguese Local Breeds
<p>Recording of the talk “A survey of pathogens on lamb carcasses from Portuguese local breeds”, presented by Ursula Gonzales-Barron at the 71<sup>st</sup> Annual Meeting of the European Federation of Animal Science, EAAP, Online virtual meeting (1-4 Dec 2020).</p>
Local male breeding density affects extra‐pair paternity in a south temperate population of grass wrens Cistothorus platensis
<p>Demographic factors can affect the frequency of extra-pair paternity (EPP) in birds, as the distribution and availability of potential mates in both space and time influence the rate of encounters between females and males. Over three breeding seasons, we intensively studied the breeding system of a south temperate population of grass wrens <i>Cistothorus platensis</i> by genotyping 73 broods (319 nestlings) and estimating EPP rates for those broods. Using five different radii (80, 160, 240, 320, and 400 m) around each nest with assigned paternity, we examined the effects of local breeding synchrony, male breeding density, and adult sex ratio (ASR) on the EPP rate. The majority of extra-pair offspring (~80%) were sired by neighboring males. Neither local breeding synchrony nor ASR consistently explained the EPP rate variation as their effects were only statistically significant within 320 m and 400 m. However, the EPP rate increased as the local male breeding density increased within every radius category, strongly suggesting that neighboring male abundance might play an important role in the extra-pair mating behavior in this species. Our study also highlights the relevance of using a local scale approach when studying mating behavior.</p>
Figure 2 in Effect of season and housing systems on various physiobehavioral attributes of local breed of rabbits (Oryctolagus cuniculus) in Southern Punjab, Pakistan
Figure 2. Mean values for meteorological attributes during different study seasons.
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>
High‐resolution genomic analysis of four local Vietnamese chicken breeds
<p>A total of 96 individuals were sampled from four populations of Vietnamese local chickens (28 Ho, 32 Dong Tao, 18 Mong, and 18 Mia) distributed in four provinces (Bac Ninh, Hung Yen, Ha Nam, and Hanoi, respectively) in the North of Vietnam. All individuals were from the same conservation program in Vietnam, originating from either private farms or public institutions involved in this program. Neither pedigree nor phenotypic information was available. We used stratified sampling for flocks, ensuring a distance of at least 500 m between the selected flocks and random sampling of one or two individuals in each selected flock. Genomic DNA was extracted from the blood samples of all chickens. The HD array for chickens allows for the simultaneous genotyping of approximately 580,000 SNPs. This array comprises SNPs on 28 autosomal chromosomes, two sex chromosomes (Z and W for poultry), and two linkage groups (LGE64 and LGE 22C19W28). Only SNPs on the 28 autosomes were considered in the present study. The SNPs with more than 10% missing genotypes or minor allele frequencies lower than 1% were removed, yielding a consensus panel of 454,297 autosomal SNPs for the analysis of population genetic structure.</p> <p>We applied a second quality control within each breed. Specifically, SNPs with within-breed minor allelic frequencies lower than 0.05 or SNPs with significant (P < 0.0001) deviation from the Hardy-Weinberg equilibrium were filtered out. This second filter led to 368,652, 383,792, 405,535, and 432,631 SNPs for Ho, Dong Tao, Mong, and Mia breeds, respectively. Of note, removing monomorphic SNPs within breeds may lead to the elimination of SNPs that are polymorphic across breeds. Due to the large number of available SNPs, we did not consider the potential effect of these filtered markers as important for subsequent analyses. Genetic diversity analyses were performed on the remaining 308,307 SNPs shared by all four breeds.</p>
High‐resolution genomic analysis of four local Vietnamese chicken breeds
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Local male breeding density affects extra‐pair paternity in a south temperate population of grass wrens Cistothorus platensis
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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
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Data from: Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls
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Data from: Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds
A dataset consisting of 787 animals with high density SNP chip genotypes (346,774 SNP) and 939 animals with medium density SNP chip genotypes (33,828 SNP) from a total of 8 indigenous Swiss sheep breeds was analyzed to characterize population structures, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between FPED and FROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean FROH estimates from medium density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion we identified differences in the genetic make-up of Swiss sheep breeds and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.
Data from: Tick infestation of chicks in a seabird colony varies with local breeding synchrony, local nest density and habitat structure
Parasites are a major risk for group-living animals and seabirds are notoriously susceptible to ectoparasite infestations because they commonly nest in dense colonies. Ticks parasitize seabirds across all biogeographical regions and they can be particularly harmful to nestlings, but the ecological factors that affect their transmission to chicks are little studied and poorly understood. Here we show that abundance of tick larvae in blue-footed booby (Sula nebouxii) broods varies with local nest synchrony and density, and also with habitat structure: abundance increased with local breeding synchrony, was linearly and quadratically related to local nest density, and was highest toward the southern end of the study area which has suitable (boulder-rich) habitat for ticks. Also, with increasing chick age infestation first increased and then declined. The results of this study highlight how local physical and social environmental factors influence infestation of seabird nestlings by ticks.
Data from: Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate
Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca x P. engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid ancestry, adaptive traits and climate to understand the implications of selective breeding for climate adaptations and assisted gene flow strategies. The effects of selection on associations among hybrid index estimated from ~6500 SNPs, adaptive traits, and provenance climates were assessed for ~2400 common garden seedlings. Hybrid index differences between natural and selected seedlings within breeding zones were small in Alberta (average +2%), but larger and more variable in BC (average -7 %, range -24% to +1%), slightly favoring P. glauca ancestry. The average height growth gain of selected seedlings over natural seedlings within breeding zones was 36% (range 12% to 86%). Clines in growth with temperature-related variables were strong, but differed little between selected and natural populations. Seedling hybrid index and growth trait associations with evapotranspiration-related climate variables were stronger in selected than in natural seedlings, indicating possible pre-adaptation to drier future climates. Associations among cold hardiness, hybrid ancestry and cold-related climate variables dominated signals of local adaptation that were preserved in breeding populations. Strong hybrid ancestry-phenotype-climate associations suggest that assisted gene flow will be necessary to match interior spruce breeding populations with shifting future climates. The absence of antagonistic selection responses among traits and maintenance of cold adaptation in selected seedlings suggests breeding populations can be safely redeployed using assisted gene flow prescriptions similar to those of natural populations.
Data from: A genome‐wide search for local adaptation in a terrestrial‐breeding frog reveals vulnerability to climate change
Terrestrial‐breeding amphibians are likely to be vulnerable to warming and drying climates, as their embryos require consistent moisture for successful development. Adaptation to environmental change will depend on sufficient genetic variation existing within or between connected populations. Here, we use Single Nucleotide Polymorphism (SNP) data to investigate genome‐wide patterns in genetic diversity, gene flow and local adaptation in a terrestrial‐breeding frog (Pseudophryne guentheri) subject to a rapidly drying climate and recent habitat fragmentation. The species was sampled across 12 central and range‐edge populations (192 samples), and strong genetic structure was apparent, as were high inbreeding coefficients. Populations showed differences in genetic diversity, and one population lost significant genetic diversity in a decade. More than 500 SNP loci were putatively under directional selection, and 413 of these loci were correlated with environmental variables such as temperature, rainfall, evaporation and soil moisture. One locus showed homology to a gene involved in the activation of maturation in Xenopus oocytes, which may facilitate rapid development of embryos in drier climates. The low genetic diversity, strong population structuring and presence of local adaptation revealed in this study shows why management strategies such as targeted gene flow may be necessary to assist isolated populations to adapt to future climates.
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.
FIGURE1. Breeding, migrating and wintering distributions of Palearctic Anthus [rubescens] japonicus and Nearctic Anthus rubescens rubescens/alticola subspecies groups (from BirdLife International 2022; illustration @Andrew Birch). Circles indicate origins of sequenced individuals and triangles indicate origins of analysed recordings of calls. Localities outside of the usual range of the species complex (e.g., Ireland, Oman and Israel) are not figured here. in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE1. Breeding, migrating and wintering distributions of Palearctic Anthus [rubescens] japonicus and Nearctic Anthus rubescens rubescens/alticola subspecies groups (from BirdLife International 2022; illustration @Andrew Birch). Circles indicate origins of sequenced individuals and triangles indicate origins of analysed recordings of calls. Localities outside of the usual range of the species complex (e.g., Ireland, Oman and Israel) are not figured here.
Data from: Limited influence of local and landscape factors on finescale gene flow in two pond-breeding amphibians
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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.