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2,608 results for “breed”
Data from: Recovery of native genetic background in admixed Populations Using haplotypes, phenotypes, and pedigree information – using Cika cattle as a case breed
The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.
Data from: Cooperative breeding favours maternal investment in size over number of eggs in spiders
The transition to cooperative breeding may alter maternal investment strategies depending on density of breeders, extent of reproductive skew and allo-maternal care. Change in optimal investment from solitary to cooperative breeding can be investigated by comparing social species with non-social congeners. We tested two hypotheses in a mainly semelparous system: that social, cooperative breeders, compared to subsocial, solitarily breeding congeners, 1) lay fewer and larger eggs because larger offspring compete better for limited resources and become reproducers; 2) induce egg size variation within clutches as a bet-hedging strategy to ensure that some offspring become reproducers. Within two spider genera, Anelosimus and Stegodyphus, we compared species from similar habitats and augmented the results with a mini-meta-analysis of egg numbers depicted in phylogenies. We found that social species indeed laid fewer, larger eggs than subsocials, while egg size variation was low overall, giving no support for bet-hedging. We propose that the transition to cooperative breeding selects for producing few, large offspring because reproductive skew and high density of breeders and young create competition for resources and reproduction. Convergent evolution has shaped maternal strategies similarly in phylogenetically distant species and directed cooperatively breeding spiders to invest in quality rather than quantity of offspring.
Data from: Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds
A 378-bp section of the mitochondrial displacement loop was used to estimate genetic diversity in the native Canadian equine populations. The inclusion of 10 Mountain and Moorland, 3 Nordic pony breeds, 2 feral populations, and 5 horse breeds were also investigated as they may have influenced the development (or rejuvenation) of the native Canadian populations. A total of 281 samples were sequenced, which produced 75 haplotypes derived from 54 informative sites. On further investigation, 36 of these 75 haplotypes were found to be previously unreported. Overall, total diversity was lowest in the feral Sable Island population with a haplotype diversity (0.27 ± 0.12), nucleotide diversity (0.0007 ± 0.0004), and pairwise difference of 0.286 ± 0.317. This is not surprising due to the geographic isolation of this population. Haplotype diversity was highest (1.00 ± 0.13) in the New Forest population, pairwise difference was highest (8.061 ± 4.028) in the Icelandic breed, whereas nucleotide diversity was highest in the Exmoor breed (0.0209 ± 0.0025). Within the Canadian populations, haplotype diversity was highest in the Newfoundland pony (0.96 ± 0.08), whereas pairwise difference and nucleotide diversity was highest in the Canadian horse (7.090 ± 3.581 and 0.0188 ± 0.0042, respectively). Three different estimates of genetic distances were used to examine the phylogenetic relationships amongst these populations. All 3 estimates produced similar topologies. In general, the native Canadian populations were highly represented in the D clade, with particular emphasis in the D1 and D2 clades. This is an important factor when considering the phylogenetic conservation of these Canadian equine populations.
Data from: Novel insights into relationships between egg corticosterone and timing of breeding revealed by LC-MS/MS
Inter- and intra-clutch variation in egg corticosterone (CORT), the major glucocorticoid in birds, may provide insights into how maternal stress levels vary with the timing of breeding and with laying order. Common analytical methods (e.g. immunoassays), however, suffer from cross-reaction with other steroids, leading to potential overestimation of CORT concentrations which can obscure true hormone–environment relationships and complicate among-study comparisons. We here apply a new LC-MS/MS technique, which has recently been shown to avoid the problem of cross-reactivity due to its high specificity, to quantify CORT concentrations in yolk and albumen in clutches of lesser black-backed gulls Larus fuscus. We found that CORT concentration exhibited a previously unreported U-shaped relationship with time of breeding, which we explain as a potential interplay of two forces exerting extra strain on the early and late breeders. Furthermore, results showed an increase in CORT with laying order indicating the energetic expense of egg production. The levels of CORT assessed in this study were significantly lower than those previously reported in studies using immunoassays for CORT analysis. This supports the fact that incorporating chromatography effectively reduces overestimation of CORT due to cross-reactivity with other steroid hormones, particularly in egg yolk.
Data from: Linking oceanographic conditions, migratory schedules and foraging behaviour during the non‐breeding season to reproductive performance in a long‐lived seabird
1. Studies of the mechanisms underlying climate-induced population changes are critically needed to better understand and accurately predict population responses to climate change. Long-lived migratory species might be particularly vulnerable to climate change as they are constrained by different climate conditions and energetic requirements during the breeding and non-breeding seasons. Yet, most studies primarily focus on the breeding season of these species lifecycle. Environmental conditions experienced in the non-breeding season may have downstream effects on the other stages of the annual lifecycle. Not investigating such effects may potentially lead to erroneous inferences about population dynamics. 2. Combining demographic and tracking data collected between 2006 and 2013 at Kerguelen Island on a long-lived migratory seabird, the Black-Browed Albatross (Thalassarche melanophris), we investigated the links between sea surface temperature during the non-breeding season and behavioural and phenological traits (at-sea behaviour and migratory schedules) while accounting for different responses between birds of different sex and reproductive status (previously failed or successful breeders). We then explored if variation in the foraging behaviour and timing of spring migration influenced subsequent reproductive performance. 3. Our results showed that foraging activity and migratory schedules varied by both sex and reproductive status suggesting different energetic requirements and constraints among individuals. Higher sea surface temperatures during late winter, assumed to reflect poor winter conditions, were associated with an earlier departure from the wintering grounds and an extended pre-breeding period. However, an earlier spring migration and an earlier return to Kerguelen grounds were associated with a lower breeding success. 4. Our results highlighted that behaviour during some periods of the non-breeding season, particularly towards the end of the wintering period and the pre-breeding period had a significant effect on the subsequent reproductive success. Therefore, caution needs to be given to all stages of the annual cycle when predicting the influence of climate on population dynamics.
Data from: Clinal variation in colony breeding structure and level of inbreeding in the subterranean termites Reticulitermes flavipes and R. grassei
Social insects exhibit remarkable variation in their colony breeding structures, both within and among species. Ecological factors are believed to be important in shaping reproductive traits of social insect colonies, yet there is little information linking specific environmental variables with differences in breeding structure. Subterranean termites (Rhinotermitidae) show exceptional variation in colony breeding structure, differing in the number of reproductives and degree of inbreeding; colonies can be simple families headed by a single pair of monogamous reproductives (king and queen) or they can be extended families headed by multiple inbreeding neotenic reproductives (wingless individuals). Using microsatellite markers, we characterized colony breeding structure and levels of inbreeding in populations over large parts of the range of the subterranean termites Reticulitermes flavipes in the USA and R. grassei in Europe. Combining these new data with previous results on populations of both species, we found that latitude had a strong effect on the proportion of extended-family colonies in R. flavipes and on levels of inbreeding in both species. We examined the effect of several environmental variables that vary latitudinally; while the degree of inbreeding was greatest in cool, moist habitats in both species, seasonality affected the species differently. Inbreeding in R. flavipes was most strongly associated with climatic variables (mean annual temperature and seasonality), whereas nonclimatic variables, including the availability of wood substrate and soil composition, were important predictors of inbreeding in R. grassei. These results are the first showing that termite breeding structure is shaped by local environmental factors and that species can vary in their responses to these factors.
Data from: The diet of an endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci, breeding at the Banc d'Arguin, Mauritania
In the period 1998–2010 the endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci breeding in Mauritania has decreased in numbers considerably. The causes for this decline are unknown. This study aimed to investigate the diet of the species. We analysed faecal material collected in the breeding colonies in 8 different years. The results show that Mauritanian Spoonbills almost exclusively eat shrimp (59.7%) and small fish (35.4%), the latter being dominated by Gobiidae (20.8%), Soleidae (4.8%) and Mugilidae (2.8%). Another 10 fish families were represented in small proportions. Shrimp were quantified on the basis of (parts of) mandibles present in the samples. All prey items eaten by the Spoonbills were extremely small. Diet composition of adult birds and chicks appeared to be similar. There was great variation in diet composition of adults between years, but there was no trend in any of the major diet components over the study period. This indicates that the decline of the Spoonbill population is not correlated with changes in food composition. Our diet study has been of a qualitative nature. Considering the dramatic population decline we plea for a more detailed ecological study of the species, including a quantitative approach of food intake and foraging conditions.
Data from: Natal and breeding philopatry of female Steller sea lions in southeastern Alaska
Information on drivers of dispersal is critical for wildlife conservation but is rare for long-lived marine mammal species with large geographic ranges. We fit multi-state mark-recapture models to resighting data of 369 known-aged Steller sea lion (Eumetopias jubatus) females marked as pups on their natal rookeries in southeastern Alaska from 1994-2005 and monitored from 2001-15. We estimated probabilities of females being first observed parous at their natal site (natal philopatry), and of not moving breeding sites among years (breeding philopatry) at large (> 400 km, all five rookeries in southeastern Alaska) and small (< 4 km, all islands within the largest rookery, Forrester Island Complex, F) spatial scales. At the rookery scale, natal philopatry was moderately high (0.776-0.859) for most rookeries and breeding philopatry was nearly 1, with < 3% of females switching breeding rookeries between years. At more populous islands at F, natal philopatry was 0.500-0.684 versus 0.295-0.437 at less populous islands, and breeding philopatry was 0.919-0.926 versus 0.604-0.858. At both spatial scales, the probability of pupping at a non-natal site increased with population size of, and declined with distance from, the destination site. Natal philopatry of < 1 would increase gene flow, improve population resilience, and promote population recovery after decline in a heterogeneous environment. Very high breeding philopatry suggests that familiarity with neighboring females and knowledge of the breeding site (the topography of pupping sites and nearby foraging locations) may be a critical component to reproductive strategies of sea lions.
Population structure and genetic diversity of sheep breeds in the Kyrgyzstan
<p><span>Sheep are a main livestock </span><span>species of Kyrgyzstan, a Central Asian country with predominating mountain terrain. </span>The current gene pool of local sheep resources has been forming under diverse climate conditions from the era of the trading caravans of the Great Silk Road, through the Soviet period of <span>large-scale livestock improvements</span>, which was followed by the deep crisis at the end of the 20th century, up to now. However, not much is known about the genetic background and variability of the local sheep populations. Therefore, our aims were to provide a characterization of the population structure and genetic relations within the Kyrgyz sheep breeds and to study their genetic connections with the global sheep breeds using SNP analysis. Samples of the Alai (n=31), Gissar (n=30), Kyrgyz coarse wool (n=13), Aykol (n=31), and Tien-Shan (n=24) breeds were genotyped with the OvineSNP50 BeadChip or the <span>Ovine Infinium HD BeadChip </span>(Illumina Inc., USA). The measure of inbreeding based on runs of homozygosity showed a minimum value in the Aykol breed (F<sub>ROH</sub> = 0.034), while the maximum was found in the Alai breed (F<sub>ROH</sub> = 0.071). Short ROH segments (ROH≤4Mb) were predominant in all breeds. Long ROH segments (ROH>16Mb) were absent in the Gissar breed. The Gissar and Aykol breeds had the highest values of the effective population sizes estimated for five generations ago (<i>Ne<sub>5</sub>=</i>660 and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values (<i>Ne<sub>5</sub> </i>=176 and 128, respectively). The synthetic origin of the Aykol breed was clearly evidenced by all analyses applied. Based on the network and admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan and the Russian semi-fine wool breeds demonstrated a common ancestry that most likely is due to a contribution of the Lincoln breed. The Gissar, Aykol and Kyrgyz coarse wool breeds showed a genetic background predominating in sheep populations from Iran and China whereas the Alai demonstrated the different ancestry type. The revealed admixture patterns probably resulted from the exchange and trade during the era of the Great Silk Road, which partly overlapped with historical and archeological findings.</p>
Data from: Joint estimation of survival and breeding probability in female dolphins and calves with uncertainty in state assignment
While the population growth rate in long-lived species is highly sensitive to adult survival, reproduction can also significantly drive population dynamics. Reproductive parameters can be challenging to estimate as breeders and non-breeders may vary in resighting probability and reproductive status may be difficult to assess. We extended capture–recapture (CR) models previously fitted for data on other long-lived marine mammals to estimate demographic parameters while accounting for detection heterogeneity between individuals and state uncertainty regarding reproductive status. We applied this model to data on 106 adult female bottlenose dolphins observed over 13 years. The detection probability differed depending on breeding status. Concerning state uncertainty, offspring were not always sighted with their mother, and older calves were easier to detect than young-of-the-year (YOY), respectively 0.79 (95% CI 0.59–0.90) and 0.58 (95% CI 0.46–0.68). This possibly led to inaccurate reproductive status assignment of females. Adult female survival probability was high (0.97 CI 95% 0.96–0.98) and did not differ according to breeding status. Young-of-the-year and 1-year-old calves had a significantly higher survival rate than 2-year-old (respectively 0.66 CI 95% 0.50-0.78 and 0.45 CI 95% 0.29–0.61). This reduced survival is probably related to weaning, a period during which young are exposed to more risks since they lose protection and feeding from the mother. The probability of having a new YOY was high for breeding females that had raised a calf to the age of 3 or lost a 2-year-old calf (0.71, CI 95% 0.45– 0.88). Yet this probability was much lower for non-breeding females and breeding females that had lost a YOY or a 1-year-old calf (0.33, 95% CI 0.26–0.42). The multievent CR framework we used is highly flexible and could be easily modified for other study questions or taxa (marine or terrestrial) aimed at modelling reproductive parameters.
Data from: Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)
Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (Ne). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine the breeding system of the spring-spawning European grayling Thymallus thymallus from a small Norwegian stream using parentage assignment based on the genotyping of 19 polymorphic microsatellite loci. In total 895 individual grayling fry and 154 mature grayling (57 females and 97 males) were genotyped. A total of 466 offspring were assigned a father, a mother, or a parent pair with a confidence of 90% or higher. Successfully reproducing males had on average 11.9 ± 13.3 (SD) offspring with on average 2.1 ± 1.2 partners, whereas successful females had on average 9.5 ± 12.8 offspring and 2.3 ± 1.5 partners. Parents with more partners also produced more offspring. Thus the grayling breeding system within this small stream revealed a polygynandrous breeding system, similar to what has been observed for many other salmonid fish species. The present study thus unambiguously corroborates a polygynadrous breeding system in the European grayling. This knowledge is critical for managing populations of this species, which has suffered significant local population declines throughout its range over the last several decades.
Data from: Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
Data from: Cooperative breeding influences the number and type of vocalizations in avian lineages
Although communicative complexity is often predicted to correlate with social complexity in animal societies, few studies have employed large-scale comparative analyses to test whether socially complex species have more complex systems of communication. I tested this social complexity hypothesis in birds (Class: Aves) using the large amount of natural history information that describes both vocal repertoire and social system in these species. To do so, I marshalled data from primary and secondary records of avian vocal repertoires (n = 253), and for each of the species in the dataset I recorded the reported repertoire size and associated species information. Using phylogenetic comparative methods, I found that cooperative breeding was a strong and repeatable predictor of vocal repertoire size, while other social variables, e.g. group size and group stability, had little or no influence on repertoire size. Importantly, repertoire sizes expanded concurrently with the evolution of cooperative breeding, suggesting a direct link between these two traits. Cooperatively breeding species devoted significantly more of their repertoire to contact calls and alarm calls. Overall, these results therefore lend support to the hypothesis that social complexity via behavioural coordination leads to increases in vocal complexity.
Data from: Kin-bias, breeding site selection, and female fitness in a cannibalistic Neotropical frog
Resource availability influences sexual selection within populations and determines whether behaviours such as territoriality or resource sharing are adaptive. In Thoropa taophora, a frog endemic to the Atlantic Coastal Rainforest of Brazil, males compete for and defend limited breeding sites while females often share breeding sites with other females; however, sharing breeding sites may involve costs due to cannibalism by conspecific tadpoles. We studied a breeding population of T. taophora to determine (i) whether this species exhibits polygynous mating involving female choice for territorial males and limited breeding resources; (ii) whether limited breeding resources create the potential for male–male cooperation in defence of neighbouring territories; and (iii) whether females sharing breeding sites exhibit kin-biased breeding site choice, possibly driven by fitness losses due to cannibalism among offspring of females sharing sites. We used microsatellites to reconstruct parentage and quantify relatedness at eight breeding sites in our focal population, where these sites are scarce, and in a second population, where sites are abundant. We found that at localities where the appropriate sites for reproduction are spatially limited, the mating system for this species is polygynous, with typically two females sharing a breeding site with a male. We also found that females exhibit negative kin-bias in their choice of breeding sites, potentially to maximize their inclusive fitness by avoiding tadpole cannibalism of highly related kin. Our results indicate that male territorial defence and female site sharing are likely important components of this mating system, and we propose that kinship-dependent avoidance in mating strategies may be more general than previously realized.
Figure 3 in Breeding preferences in the treefrogs Dryophytes japonicus (Hylidae) in Mongolia
Figure 3. Graph representative of the preference in water body type for breeding by Dryophytes japonicus. The species was found breeding in unused quarries, oxbow lakes and ponds.
Figure 2 in Breeding preferences in the treefrogs Dryophytes japonicus (Hylidae) in Mongolia
Figure 2. Map of sites where Dryophytes japonicus was found. Because of scale, the central image is divided in two by the dashed line. Bottom and top right image are enlargements of the central image. Note that sites 14–2 and 14–4 were not connected when sampled, in contradiction to the satellite map. Only the northernmost parts of both sites were flooded, such as drawn in white. Landscape image credits to © 2017 DigitalGlobe.
Figure 1 in Breeding preferences in the treefrogs Dryophytes japonicus (Hylidae) in Mongolia
Figure 1. Sampled locations for occurrence of Dryophytes japonicus in June 2017. The occurrence of the species was determined through call surveys and sampling of tadpoles. Presence is annotated in red and absence in green.
FIGURE 3 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 3. (A) Palmar, and (B) plantar views of right hand and foot of the holotype of Osteocephalus castaneicola sp. n. (CBF 6051). Scale bar equals 5 mm.
FIGURE 4 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 4. Schematic map of northern Bolivia showing the known distribution of Osteocephalus castaneicola sp. n. in Bolivia: (1) San Antonio del Matti, (2) San Antonio de Filadelfia (type locality).
FIGURE 1 in A new species of Osteocephalus (Anura: Hylidae) from Amazonian Bolivia: first evidence of tree frog breeding in fruit capsules of the Brazil nut tree
FIGURE 1. The majority rule consensus tree of the Bayesian phylogeny of the frog genus Osteocephalus, using mitochondrial 12S rRNA – tRNA-Val – 16S rRNA data. Nodal support, Bayesian posterior probabilities (BPP) and maximum likelihood (PhyML) bootstrap (1000 pseudoreplicates), are indicated. Collapsed branches were supported <50 % bootstrap and <0.50 BPP. The asterisk denotes the tadpole sample from a water-filled fruit capsule of the Brazil nut tree. Osteocephalus "oophagus" no. AF467267 may represent O. cabrerai according to Fouquet et al. (2007, Supporting Information).
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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.