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129 results for “jays”
A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri)
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How flexible is tool use in Eurasian jays (Garrulus glandarius)?
<p>Datasets and statistical analyses (R scripts) of a study on tool use in Eurasian jays. Three object-dropping experiments were conducted. Experiment 1 and 2 investigated whether jays could select functional tools (tool selectivity) according to their physical properties, respectively size and shape. Experiment 3 explored jays’ capability of using different tools – sticks – to acquire food for the same apparatus.</p>
Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays
Estimates of the timing of divergence are central to testing the underlying causes of speciation. Relaxed molecular clocks and fossil calibration have improved these estimates; however, these advances are implemented in the context of gene trees, which can overestimate divergence times. Here we couple recent innovations for dating speciation events with the analytical power of species trees, where multilocus data are considered in a coalescent context. Divergence times are estimated in the bird genus Aphelocoma to test whether speciation coincided with mountain uplift or glacial cycles. Gene trees and species trees show general agreement that diversification began in the Miocene amid mountain uplift. However, dates from the multilocus species tree are more recent, occurring predominately in the Pleistocene, consistent with theory that divergence times can be significantly overestimated with gene-tree based approaches that do not correct for genetic divergence that predates speciation. In addition to coalescent stochasticity, Haldane's Rule could account for differences in timing estimates between mitochondrial and nuclear genes. By incorporating a fossil calibration applied to the species tree, in addition to the process of gene lineage coalescence, the present approach provides a more biologically realistic framework for dating speciation events, and hence for testing the links between diversification and specific biogeographic and geologic events.
Data from: Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species
Kin recognition is a critical element to kin cooperation, and in vertebrates, it is primarily based on associative learning. Recognition of socially unfamiliar kin occurs rarely, and it is reported only in vertebrate species where promiscuity prevents recognition of first-order relatives. However, it is unknown whether the recognition of socially unfamiliar kin can evolve in monogamous species. Here, we investigate whether genetic relatedness modulates aggression among group members in Siberian jays (Perisoreus infaustus). This bird species is genetically and socially monogamous and lives in groups that are formed through the retention of offspring beyond independence, and the immigration of socially unfamiliar nonbreeders. Observations on feeders showed that genetic relatedness modulated aggression of breeders towards immigrants in a graded manner, in that they chased most intensely the immigrant group members that were genetically the least related. However, cross-fostering experiments showed that breeders were equally tolerant towards their own and cross-fostered young swapped as nestlings. Thus, breeders seem to use different mechanisms to recognize socially unfamiliar individuals and own offspring. As Siberian jays show a high degree of nepotism during foraging and predator encounters, inclusive fitness benefits may play a role for the evolution of fine-scale kin recognition. More generally, our results suggest that fine-graded kin recognition can evolve independently of social familiarity, highlighting the evolutionary importance of kin recognition for social species.
Data from: Disentangling plastic and genetic changes in body mass of Siberian jays
Spatial and temporal phenotypic differentiation in mean body size is of commonplace occurrence, but the underlying causes remain often unclear: both genetic differentiation in response to selection (or drift) and environmentally induced plasticity can create similar phenotypic patterns. Studying changes in body mass in Siberian jays (Perisoreus infaustus) over three decades, we discovered that mean body mass declined drastically (ca. 10%) over the first two decades, but increased markedly thereafter back to almost the initial level. Quantitative genetic analyses revealed that although body mass was heritable (h2 = 0.46), the pronounced temporal decrease in body mass was mainly a product of phenotypic plasticity. However, a concomitant and statistically significant decrease in predicted breeding values suggests a genetic component to this change. The subsequent increase in mean body mass was indicated to be entirely due to plasticity. Selection on body mass was estimated to be too weak to fully account for the observed genetic decline in body mass, but bias in selection differential estimates due to environmental covariance between body mass and fitness is possible. Hence, the observed body mass changes appear to be driven mainly by phenotypic plasticity. Although we were not able to identify the ecological driver of the observed plastic changes, the results highlight the utility of quantitative genetic approaches in disentangling genetic and phenotypic changes in natural populations.
Data from: Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact
Background: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. Results: Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane's Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. Conclusions: This study adds to a growing list of studies that support predictions of Haldane's Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane's Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumicrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.
Data from: Voluntary food sharing in pinyon jays: the role of reciprocity and dominance
Food sharing offers a clear example of prosocial behaviour, in which one individual's actions benefit another. Researchers have proposed a range of hypotheses that explain why food sharing may occur among unrelated individuals. Two such hypotheses, reciprocity and dominance, have been tested in many species, including fish, corvids, rats, bats and primates, showing that (1) recipients sometimes reciprocate sharing back to previous donors and (2) dominant individuals share more than subordinates. Although primates dominate the study of prosocial behaviour, active donation of food is actually quite rare in primates. In contrast, several corvid species spontaneously share food much more frequently. Here, we explored the role of reciprocity and dominance in spontaneous food sharing among male pinyon jays, Gymnorhinus cyanocephalus, a North American corvid species that exhibits high levels of social complexity. Unlike much of the previous work, we tested prosocial behaviour among unrelated, non-pair-bonded adults. We observed high levels of active sharing, and donors showed clear preferences with whom they shared. We found no evidence that pinyon jays reciprocated shares in either the short or long term. This was true for both sharing within dyads (direct reciprocity) and sharing irrespective of most recent partner identity (generalized reciprocity). However, dominance influenced sharing in one of our squads, with dominant individuals sharing more than subordinates. This study highlights corvids as a fruitful model for the study of the proximate mechanisms underlying naturally occurring prosocial behaviours.
No evidence for future planning in Canada Jays (Perisoreus canadensis)
In the past 20 years, research in animal cognition has challenged the belief that complex cognitive processes are uniquely human. At the forefront of these challenges has been research on mental time travel and future planning in jays. We tested whether Canada Jays (<i>Perisoreus canadensis</i>) demonstrated future planning, using a procedure that had previously produced evidence of future planning in California Scrub-Jays (Aphelocoma californica). Future planning in this procedure is caching in locations where the bird will predictably experience a lack of food in the future. Canada Jays showed no evidence of future planning in this sense and instead placed caches in a location where food was usually available, the opposite of the behaviour described for California Scrub-Jays. We provide potential explanations for these differing results and suggest a re-evaluation of "complex cognition" as an explanation of caching behaviour in jays.
Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays
<p class="MsoNormal"><span>Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-jays in the genus <em>Aphelocoma</em> provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (<em>A. w. sumichrasti</em>), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage <em>A. w. texana</em>, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (<em>A. californica</em>) and Woodhouse's Scrub-Jay (<em>A. woodhouseii</em>), result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting to better understand the systematics of other groups with similarly complex evolutionary histories.</span></p>
Family Reunion by The O'Jays
<p>Introdcution to methodology chapter in <em>Fragmented to Whole </em>dissertation</p>
Data from: Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays
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Cache site exploitations by Canada jays (Perisoreus canadensis)
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Data from: Disentangling plastic and genetic changes in body mass of Siberian jays
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Data from: Speciation in Western Scrub-Jays, Haldane’s rule, and genetic clines in secondary contact
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Data from: Fine-scale kin recognition in the absence of social familiarity in the Siberian jay, a monogamous bird species
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Combining species delimitation, species trees, and tests for gene flow illuminates complex speciation in scrub-jays
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Data from: Mesotocin influences pinyon jay prosociality.
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Data from: Voluntary food sharing in pinyon jays: the role of reciprocity and dominance
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Data from: Autumn freeze-thaw events carry over to depress late-winter reproductive performance in Canada Jays
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No evidence for future planning in Canada Jays (Perisoreus canadensis)
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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.