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100 Years of Penaeids Domestication and Meta-analysis of Breeding Traits
<p><strong>Additional files</strong></p> <p><strong>Additional file 1 Table S1</strong></p> <p>Format: csv file</p> <p>Title: Quantitative genetic publications for penaeids genetic improvement programs from 1997 to 2024.</p> <p><strong>Additional file 2 Table S2</strong></p> <p>Format: csv file</p> <p>Title: Summary of heritability estimates on breeding traits in penaeids selective breeding programs.</p> <p><strong>Additional file 3 Table S3</strong></p> <p>Format: csv file</p> <p>Title: Analysis of heritability estimates in penaeids selective breeding programs for disaese resistance, feeding efficiency, growth traits, morphological traits, quality traits, reproductive traits, stress tolerance and survival.</p>
Egg size is unrelated to ambient temperature in the opportunistically breeding zebra finch
In many birds, there is significant variation in egg size both across and within clutches that remains to be explained. Birds lay one egg per day and in hot climates, the first laid eggs may start to develop before the laying of the rest of the clutch is complete, through warming by the ambient air temperature. Here, we test the hypothesis that in hot conditions, skews in egg size across the laying sequence may be more pronounced, as females use egg size to compensate for hatching asynchrony, providing a higher level of provisioning to the later laid eggs that would hatch later due to ambient incubation. We have focused on the zebra finch (Taeniopygia guttata), a species that typically breeds over an extended period of the year, and therefore across a particularly wide range of ambient temperatures. We characterised the variation in egg size using data from over 700 clutches, including historical specimens, a wild population, and both domesticated and wild birds breeding in captivity, in addition to clutches produced experimentally in controlled-temperature rooms. Here, we document significant variation in egg size between and within clutches, with eggs increasing in size over the laying order, with both maternal identity and population differences playing an important role (domesticated birds laid eggs that were much larger than their wild counterparts). However, we found no support for the idea that variation in egg size either within a clutch, and across clutches and populations, is related to variation in ambient temperature, despite the large range of thermal environments experienced during laying. In conclusion, whilst egg size is clearly a labile characteristic there is no evidence this is flexibly adjusted to local ambient temperatures before and during laying.
Data from: Interaction among ploidy, breeding system, and lineage diversification
If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit twenty-nine diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole-genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.
Multilayer social networks reveal the social complexity of a cooperatively breeding bird
<p>Focal observations of Arabian babblers (<em>Argya squamiceps</em>). The folder contains adjacency matrices of nine social groups observed between 2017 and 2020. Some of the groups were observed multiple times, the complete list of group rounds is also provided. We recorded six different interaction types, hence the folder contains a total of 114 adjacency matrices.</p>
Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle
<p>Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. Whilst there have been many genome-wide association studies (GWAS) conducted on FT-MIR predicted traits, there have been few GWAS for individual FT-MIR wavenumbers. Here we examine associations between genomic regions and individual FT-MIR wavenumber phenotypes within a population of 38,085 mixed-breed New Zealand dairy cattle with imputed whole-genome sequence. GWAS were conducted for each of 895 individual FT-MIR wavenumber phenotypes and three FT-MIR predicted milk composition traits, and gene annotation and mammary tissue gene expression datasets were employed to identify candidate causative genes and variants. This resulted in the identification of 38 co-locating, co-segregating expression QTL (eQTL), and 31 protein-sequence mutations for FT-MIR wavenumber phenotypes, the latter including a null mutation in <i>ABO</i> that has a potential role in changing milk oligosaccharide profiles. For the candidate causative genes implicated in these analyses, the strength of association between relevant loci and each wavenumber across the mid-infrared spectrum revealed shared association patterns for groups of genomically-distant loci, highlighting clusters of loci linked through their biological roles in lactation and their presumed impacts on the chemical composition of milk.</p>
A small vocal repertoire during the breeding season expresses complex behavioral motivations and individual signature in the Common Coot
<p><b>Backgroun</b><b>d:</b> Although acoustic communication plays an essential role in the social interactions of Rallidae, our knowledge of how Rallidae encode diverse types of information using simple vocalizations is limited. We recorded and examined the vocalizations of a Common Coot (<i>Fulica atra</i>) population during the breeding season to test the hypotheses that 1) different call types can be emitted under different behavioral contexts, and 2) variation in the vocal structure of a single call type may be influenced both by behavioral motivations and individual signature. We measured a total of 61 recordings of 30 adults while noting the behavioral activities in which individuals were engaged. We compared several acoustic parameters of the same call type emitted under different behavioral activities to determine how frequency and temporal parameters changed depending on behavioral motivations and individual differences.</p> <p><b>Results: </b>We found that adult Common Coots had a small vocal repertoire, including 4 types of call, composed of a single syllable that was used during 9 types of behaviors. The 4 calls significantly differed in both frequency and temporal parameters and can be clearly distinguished by discriminant function analysis. Minimum frequency of fundamental frequency (F<sub>0min</sub>) and duration of syllable (T) contributed the most to acoustic divergence between calls. Call <i>a</i> was the most commonly used (in 8 of the 9 behaviors detected), and maximum frequency of fundamental frequency (F<sub>0max</sub>) and interval of syllables (TI) contributed the most to variation in call <i>a</i>. Duration of syllable (T) in a single call <i>a</i> can vary with different behavioral motivations after individual vocal signature being controlled.</p> <p><b>Conclusions:</b> These results demonstrate that several call types of a small repertoire, and a single call with function-related changes in the temporal parameter in Common Coots could potentially indicate various behavioral motivations and individual signature. This study advances our knowledge of how Rallidae use "simple" vocal systems to express diverse motivations and provides new models for future studies on the role of vocalization in avian communication and behavior.</p>
From individual to population level: Temperature and snow cover modulate fledging success through breeding phenology in Greylag geese (Anser anser)
<p>Local weather conditions may be used as environmental cues by animals to optimize their breeding behaviour, and could be affected by climate change. We measured associations between climate, breeding phenology, and reproductive output in greylag geese (<i>Anser anser</i>) across 29 years (1990-2018). The birds are individually marked, which allows accurate long-term monitoring of life-history parameters for all pairs within the flock. We had three aims: (1) identify climate patterns at a local scale in Upper Austria, (2) measure the association between climate and greylag goose breeding phenology, and (3) measure the relationship between climate and both clutch size and fledging success. Ambient temperature increased 2°C across the 29-years study period, and higher winter temperature was associated with earlier onset of egg-laying. Using the hatch-fledge ratio, average annual temperature was the strongest predictor for the proportion of fledged goslings per season. There is evidence for an optimum time window for egg-laying (the earliest and latest eggs laid had the lowest fledging success). These findings broaden our understanding of environmental effects and population-level shifts which could be associated with increased ambient temperature and can thus inform future research about the ecological consequences of climate changes and reproductive output in avian systems.</p>
Figure 2 in Do male tree frogs feed during the breeding season? Stomach flushing of five syntopic hylid species in Rio Grande do Sul, Brazil
Figure 2. Frequency of animal items ingested by 50 calling male frogs per species.
Figure 1 in Do male tree frogs feed during the breeding season? Stomach flushing of five syntopic hylid species in Rio Grande do Sul, Brazil
Figure 1. Frequency of animal and plant items ingested by 50 calling male frogs per species.
Data - Sow what you sell: strategies for integrating organic breeding and seed production into value chain partnerships
<p>Online survey targeting organic farmers on organic seed use; 25 questions in the survey. The survey was conducted between November 2018 and June 2019 and distributed through the networks of partners involved in the Horizon2020 project LIVESEED, including 23 breeding & research institutes, seven breeding companies, eight seed companies, and 11 organic associations. 752 complete entries by farmers from 20 countries from Central, Northern, Southern and Eastern Europe could be used from the 1,475 total accesses to the survey.</p>
Fig. 6 in Observations On Breeding And Moulting Of The Grey-Eyed Bulbul, Iole Propinqua, In Thailand
Fig. 6. Primary moult score of Grey-eyed Bulbul plotted against rectrice moult score.
Figs. 1, 2 in Observations On Breeding And Moulting Of The Grey-Eyed Bulbul, Iole Propinqua, In Thailand
Figs. 1, 2. The nest of Grey-eyed Bulbul Iola propinqua.
Fig. 5 in Observations On Breeding And Moulting Of The Grey-Eyed Bulbul, Iole Propinqua, In Thailand
Fig. 5. Primary moult score of Grey-eyed Bulbul plotted against tertial moult score.
Fig. 4 in Observations On Breeding And Moulting Of The Grey-Eyed Bulbul, Iole Propinqua, In Thailand
Fig. 4. Primary moult score of Grey-eyed Bulbul plotted against secondary moult score.
Effects of released farmed mallards on species richness of breeding waterbirds and amphibians in natural, restored, and constructed wetlands
<p>Common practices in current game management are wetland restoration and creation, as well as releases of quarry species. We studied the impact of releases of mallard ducklings on species richness of wild waterbirds and amphibians on three types of wetlands: natural, constructed and restored. Data on species richness, macrophyte cover and water characteristics (total phosphorous and pH) were collected at 32 sites in an agricultural landscape in southern Sweden. In total, 14 species of waterbirds were recorded, ranging from zero to seven per wetland and survey. Amphibians were present in 24 of the 32 wetlands; in total five species were found, ranging from zero to three per wetland. By using generalized linear modelling we found that wetland type best predicted waterbird species richness. Constructed wetlands had significantly more waterbird species, regardless of whether they were used for mallard releases or not. There were breeding amphibians in 62% of natural, 100% of restored and 77% of constructed wetlands. Breeding amphibians were present in 84% of wetlands without, and in 62% of wetlands with releases. However, included variables did not explain amphibian species richness in the wetlands. Releasing large numbers of mallards on a wetland and providing food ad libitum is likely to affect water quality, nutrient availability and predation pressure. Indeed, phosphorous levels were significantly higher in release wetlands, but no differences were found between wetland types.This means that mallard releases may increase nutrient loads in environments that are already eutrophied. However, in our study system releases did not influence species richness of waterbirds and amphibians locally. Constructing wetlands for mallard releases can thus have positive local effects on species richness.</p>
Breeding biology data for two sympatric small procellariiform seabirds in south-eastern Australia
<p>Data on breeding phenology, breeding success and chick growth in sympatric common diving petrels and fairy prions in south-eastern Australia. </p>
Fig. 7 in Reproductive behavior, development and eye regression in the cave armored catfish, Ancistrus cryptophthalmus Reis, 1987 (Siluriformes: Loricariidae), breed in laboratory
Fig. 7. Summary of the life cycle of Ancistrus cryptophthalmus from Passa Três Cave.
A haplotype-led approach to increase the precision of wheat breeding
<p>Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (<em>Triticum aestivum</em>) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence alone was insufficient to fully differentiate between haplotypes, as were commonly used array-based genotyping chips due to their gene centric design. We successfully used this approach for focused discovery of novel haplotypes from a landrace collection and documented their potential for trait improvement in modern bread wheat. This study provides a framework for defining and exploiting haplotypes to increase the efficiency and precision of wheat breeding towards optimising the agronomic performance of this crucial crop.</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>
No seasonal curtailment of the Eurasian Skylark's (Alauda arvensis) breeding season in German heterogeneous farmland
<p><span>The lack of suitable nesting sites is one key driver behind the farmland bird crisis in Europe. Winter cereals become impenetrable for ground-breeding birds like the Eurasian Skylark (<em>Alauda arvensis</em>), curtailing breeding time. Stable Skylark populations depend on multiple breeding attempts per year; thus, the widespread cultivation of winter cereals has strongly contributed to their tremendous decline. Crop diversification is thought to be a potential measure to counteract this development. Therefore, we explored</span> <span>how individual Skylarks respond to the decreasing suitability of winter cereals as nesting habitat in heterogeneous but otherwise conventionally managed farmland. Our study focused on: i) the degree to which Skylarks prematurely cease nesting activity, switch nesting habitats, or breed on linear structures like tramlines. Additionally, we analyzed: ii) if nest success decreases throughout the breeding season and iii) how often Skylarks make a successful breeding attempt per year. We radio-tagged 28 adults in a German population during April 2018 and 2019, tracked half of them for more than 3 months, and measured their breeding success. Additionally, we monitored nests of untagged pairs, resulting in 96 nests found. None, except one tagged individual, stopped breeding activity before July 1st. Home ranges were mainly stable, but Skylarks switched nesting habitats away from winter cereals to crops like sugar beet or set-aside. High-risk nesting sites like corn and linear structures played a minor role in breeding. Overall, Mayfield logistic regressions revealed no seasonal decrease in nest success, and tagged Skylarks had sufficient time to make 1.5 – 1.8 breeding attempts, of which 0.8 were successful. We suggest that heterogeneous farmland in our study area, which enabled diversely composed home ranges, prevented a curtailment of the breeding season. Thus, our study reinforces the need for crop diversification which gives Skylarks a chance to survive in modern farmland. </span></p>
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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.