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Data for sperm numbers as a paternity guard in a wild bird
Sperm competition is thought to impose strong selection on males to produce competitive ejaculates to outcompete rival males under competitive mating conditions. Our understanding of how different sperm traits influence fertilization success, however, remains limited, especially in wild populations. Recent literature highlights the importance of incorporating multiple ejaculate traits and pre-copulatory sexually selected traits in analyses aimed at understanding how selection acts on sperm traits. However, variation in a male's ability to gain fertilization success may also depend upon a range of social and ecological factors that determine the opportunity for mating events both within and outside of the social pair-bond. Here, we test for an effect of sperm quantity and sperm size on male reproductive success in the red-back fairy-wren (Malurus melanocephalus) while simultaneously accounting for pre-copulatory sexual selection and potential socio-ecological correlates of male mating success. We found that sperm number (i.e., cloacal protuberance volume), but not sperm morphology, was associated with reproductive success in male red-backed fairy-wrens. Most notably, males with large numbers of sperm available for copulation achieved greater within-pair paternity success. Our results suggest that males use large sperm numbers as a defensive strategy to guard within-pair paternity success in a system where there is a high risk of sperm competition and female control of copulation. Finally, our work highlights the importance of accounting for socio-ecological factors that may influence male mating opportunities when examining the role of sperm traits in determining male reproductive success.
Data from: Emerging wild virus of native grass bioenergy feedstock is well established in the Midwestern USA and associated with premature stand senescence
<p>This dataset includes values for the prevalence of switchgrass mosaic virus (Genus Marafivirus, Family Tymoviridae) detected with molecular diagnostics (RT-PCR) in individual Panicum virgatum (switchgrass) plants and in Graminella leafhoppers that feed on them. Surveys were conducted in 15 sites in August 2012. Stands surveyed had been established for some time and represent a range of landscape contexts. Measures of stand height and percent senescence were also collected. Land cover composition surrounding each site was calculated from the USDA-NASS Cropland Data Layer and estimates of drought impact were derived from the US Drought Monitor.</p>
Tests of search image and learning in the wild: insights from sexual conflict in damselflies
<p><a name="_Hlk52373699">Search image formation, a proximal mechanism to maintain genetic polymorphisms by negative frequency-dependent selection, has rarely been tested under natural conditions. Females of many non-territorial damselflies resemble either conspecific males or background vegetation. Mate-searching males are assumed to form search images of the majority female type, sexually harassing it at rates higher than expected from its frequency, thus selectively favoring the less common morph. We tested this and how morph coloration and behavior influenced male perception and intersexual encounters by following marked <i>Ischnura elegans</i> and noting their reactions<i> </i>to conspecifics. Contrary to search image formation and associative learning hypotheses, although males </a>encountered the minority, male-like morph more often, sexual harassment and clutch size were similar for both morphs. Prior mating attempts or copulas with morphs did not affect a male's subsequent reaction to them; males rarely attempted matings with immature females or males. Females mated early in the day, reducing the opportunity for males to learn their identity beforehand. Once encountered, the male-like morph was more readily noticed by males than the alternative morph, which, once noticed was more likely to receive mating attempts. Flexible behavior gave morphs considerable control over their apparency to males, influencing intersexual encounters. Results suggested a more subtle proximal mechanism than male learning maintains these color polymorphisms and call for inferences of learning to be validated by behavior of wild receivers and their signalers.</p>
Quantifying heritability and estimating evolutionary potential in the wild when individuals that share genes also share environments
<p>Accurate heritability estimates for fitness-related traits are required to predict an organism's ability to respond to global change. Heritability estimates are theoretically expected to be inflated if, due to limited dispersal, individuals that share genes are also likely to share similar environments. However, if relatives occupy similar environments due, at least partly, to genetic variation for habitat selection, then accounting for environmental similarity in quantitative genetic models may result in diminished heritability estimates in wild populations. This potential issue has been pointed out in the literature, but has not been evaluated by empirical studies.<br><br>Here, we investigate whether environmental similarity among individuals can be partly explained by genetic variation for habitat selection, and how this link potentially blurs estimates for heritability in fitness-related traits.<br><br>Using intensive GPS-monitoring, we quantified home-range habitat composition for 293 roe deer inhabiting a heterogeneous landscape to assess environmental similarity. To investigate if environmental similarity might harbour genetic variation, we combined genome-wide data in a quantitative genetic framework to evaluate genetic variation for home-range habitat composition, which is partly the result of habitat selection at settlement. Finally, we explored how environmental similarity affects heritability estimates for behaviours related to the risk avoidance-resource acquisition trade-off (i.e. being in open habitat, distance to roads) and proxies of individual performance (i.e. body mass, hind foot length). We found substantial heritability for home-range habitat composition, with estimates ranging from 0.40 (proportion of meadows) to 0.85 (proportion of refuge habitat). Accounting for similarity in habitat composition between relatives decreased the heritability estimates for both behavioural and morphological traits (reduction ranging from 55% to 100% and from 22% to 41%, respectively). As a consequence, only half of these heritability estimates remained significantly different from zero.<br><br>Our results show that similar genotypes occupy similar environments, which could lead to heritable variation being incorrectly attributed to environmental effects. To accurately distinguish the sources of phenotypic variation and predict the ability of organisms to respond to global change, it is necessary to develop quantitative genetic studies investigating the mechanisms underpinning environmental similarity among relatives.</p>
Bash in the Wild: Language Usage, Code Smells, and Bugs - Dataset
<p>This is the data set for the paper "Bash in the Wild: Language Usage, Code Smells, and Bugs".</p>
Data from: Genetic analysis of life-history constraint and evolution in a wild ungulate population
Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.
Data from: How far is enough? Prediction of the scale of effect for wild bees
<p class="MsoNormal"><span>A crucial issue for landscape ecologists is identifying the spatial extents at which a landscape affects species occurrence. Multi-scale analyses are usually conducted to identify the "scale of effect", that is, the spatial extent associated with the best relationship between landscape variables and species occurrence, which is assumed to be related to species traits. However, few guidelines exist to determine the range of distances to be investigated.</span></p> <p class="MsoNormal"><span>Based on the foraging distances of wild bee species, our main goal was to estimate the maximum distance of effect, that is, the distance beyond which the scale of effect for wild bee species is unlikely to be detected.</span></p> <p class="MsoNormal"><span>Using the InVEST pollination model, we (i) modelled bee categories with distinct foraging distances and identified the scale of effect on their simulated abundance (ii) defined an index, noted </span><span>λ</span><span>, that estimates the distance beyond which landscape composition has only negligible effects on simulated abundances. We validated our results by identifying the scale of effect on the abundances of 16 bee species collected in south-western France.</span></p> <p class="MsoNormal"><span>We detected a significant positive relationship between the average foraging distance (</span><span>α</span><span>) of the modelled bees and their scale of effect. The </span><span>λ</span><span> index was linearly related to the average foraging distances of bees (</span><span>λ</span><span>=5.4 </span><span>α</span><span>+253) and was above the identified scale of effect for the modelled bees. The </span><span>λ</span><span> was also found to be above the scale of effect for 93% of the observed bee species.</span></p> <p><span>Our results suggest that the </span><span>λ</span><span> index is a good estimator of the upper limit of the scale of effect for wild bees. The </span><span>λ</span><span> index could be used to identify the minimum distance between sampling sites before setting up an experiment and the maximum buffer size required in multi-scale analysis to detect the scale of effect.</span></p>
Dataset for human PDI wild-type and variants labeled at positions 57/401, 88/401, 57/467, and 88/467 with Atto 550/647N
<p>PTU files (time-correlated single-photon counting data) of freely diffusing human oxidized and reduced PDI wild-type and variants labeled at positions 57/401, 88/401, 57/467, and 88/467 with Atto 550/647N. </p> <p> </p> <p> </p>
Fig. 4 in Solanum insanum L. (subgenus Leptostemonum Bitter, Solanaceae), the neglected wild progenitor of eggplant (S. melongena L.): a review of taxonomy, characteristics and uses aimed at its enhancement for improved eggplant breeding
Fig. 4 Intermediate fruit morphology of an interspecific hybrid (INS1.2 X MEL 5.5) as compared to the parental lines S. insanum (INS1) and S. melongena (MEL5)
Fig. 2 in Solanum insanum L. (subgenus Leptostemonum Bitter, Solanaceae), the neglected wild progenitor of eggplant (S. melongena L.): a review of taxonomy, characteristics and uses aimed at its enhancement for improved eggplant breeding
Fig. 2 Morphology of Solanum insanum. A Flower from wild c population in Sri Lanka (abandoned field in Anradhapura district, North Central province). B Flower from Sri Lankan accession INS2 cultivated in Spain. C Flower from accession INS3 of unknown origin cultivated in Spain. D Longitudinal section of the flower (X10) of accession INS2. E Fruit without prickly calyx (cultivated Sri Lankan accession in Spain) (accession INS2). F The fruit with prickly calyx (Sri Lankan accession INS1 cultivated in Spain). G The fruit without prickly calyx from a wild population in Sri Lanka (forest boundary in Matale district, Central province). H Longitudinal section of a fruit of accession INS1. I Microscopic view of seeds. J Stem with sharp and slightly curved prickles of accession INS1. K Prostrate form of plant from a home garden. L Adaxial surface of leaf with dark purple prickles (K, L both Anradhapura district, North Central province, Sri Lanka). (Color figure online)
Fig. 3 in Solanum insanum L. (subgenus Leptostemonum Bitter, Solanaceae), the neglected wild progenitor of eggplant (S. melongena L.): a review of taxonomy, characteristics and uses aimed at its enhancement for improved eggplant breeding
Fig. 3 Geographical distribution of Solanum insanum L. Apparent large gaps in the distribution of this very common species are due to a variety of factors. Among them are (1) our not having seen many local herbaria in India or Myanmar, (2) the lack of specificity in localities in many early collections from India (see Endersby 2008), and (3) possible collecting deficit, especially in Myanmar and Sumatra
Fig. 1 in Solanum insanum L. (subgenus Leptostemonum Bitter, Solanaceae), the neglected wild progenitor of eggplant (S. melongena L.): a review of taxonomy, characteristics and uses aimed at its enhancement for improved eggplant breeding
Fig. 1 Morphology of Solanum insanum. A Branch with prickles and mature leaves. B Hermaphroditic flower. C Mature fruit with prickly calyx. Drawn in the field from a weedy plant in Anradhapura district, North Central province, Sri Lanka. Illustration by I. Peabotuwage
Distribution. Sub-Saharan Africa; virtually eradicated from W Africa, and greatly reduced in C and NE Africa. The largest populations exist in Botswana, Tanzania, and Zimbabwe, which account for approximately half of the estimated number of African Wild Dogs remaining in the wild. Other populations occur in Central African Republic, Ethiopia, Kenya, Mozambique, Namibia, South Africa, Sudan, and Zambia. Potential small populations (less than 100 individuals) may exist in Cameroon, Chad, Senegal, and Somalia. in Canidae
Distribution. Sub-Saharan Africa; virtually eradicated from W Africa, and greatly reduced in C and NE Africa. The largest populations exist in Botswana, Tanzania, and Zimbabwe, which account for approximately half of the estimated number of African Wild Dogs remaining in the wild. Other populations occur in Central African Republic, Ethiopia, Kenya, Mozambique, Namibia, South Africa, Sudan, and Zambia. Potential small populations (less than 100 individuals) may exist in Cameroon, Chad, Senegal, and Somalia.
Subspecies and Distribution. C. lupus Linnaeus, 1758 - Asia, Europe. C. l. albus Kerr, 1792 — N Russia. C. l. arctos Pocock, 1935 — Canadian High Arctic. C. l. baileyi Nelson & Goldman, 1929 — Mexico, SW USA (extinct in the wild). C. l. communis Dwigubski, 1804 — C Russia. C. l. cubanensis Ognev, 1923 — E-C Asia. C. l. dingo Meyer, 1793 — SE Asia and Australasia. C. l. lycaon Schreber, 1775 — SE Canada, NE USA. C. l. nubilus Say, 1823 — E-C Canada and C USA. C. l. occidentalis Richardson, 1829 — Alaska, NW Canada. C. l. pallipes Sykes, 1831 — Middle East and SW Asia to India. in Canidae
Subspecies and Distribution. C. lupus Linnaeus, 1758 - Asia, Europe. C. l. albus Kerr, 1792 — N Russia. C. l. arctos Pocock, 1935 — Canadian High Arctic. C. l. baileyi Nelson & Goldman, 1929 — Mexico, SW USA (extinct in the wild). C. l. communis Dwigubski, 1804 — C Russia. C. l. cubanensis Ognev, 1923 — E-C Asia. C. l. dingo Meyer, 1793 — SE Asia and Australasia. C. l. lycaon Schreber, 1775 — SE Canada, NE USA. C. l. nubilus Say, 1823 — E-C Canada and C USA. C. l. occidentalis Richardson, 1829 — Alaska, NW Canada. C. l. pallipes Sykes, 1831 — Middle East and SW Asia to India.
Interaction of diet and habitat predicts Toxoplasma gondii infection rates in wild birds at a global scale
<p><b>Aim:</b> Free-ranging wildlife are valuable sentinels for zoonotic, multi-host pathogens, and novel insight on parasite transmission patterns is possible through a macroecological approach. <i>Toxoplasma gondii</i> is a protozoan capable of infecting all warm-blooded animals, including humans, primarily through a free-living oocyst and/or tissue cyst life-stage. Anthropogenic disturbance is facilitating the spread of <i>T. gondii</i>, making it critical to understand the general ecological and life history drivers of <i>T. gondii</i> infections in wild birds, which are important intermediate hosts. Our goal was to determine how habitat (terrestrial vs. aquatic), dietary trophic level and scavenging behaviour influence <i>T. gondii</i> infection prevalence in wild birds on a global scale.</p> <p><b>Location: </b>Global</p> <p><b>Time period: </b>1952-2017</p> <p><b>Major taxa studied: </b>Birds</p> <p><b>Methods</b>: Our analysis used the serological, bioassay and molecular prevalence data of <i>T. gondii</i> in avian species compiled from 81 studies conducted worldwide and encompassing 24,344 individuals from 393 avian species from 84 families.</p> <p><b>Results: </b>We show that at a global scale, trophic level and habitat significantly interact to influence <i>T. gondii </i>prevalence in avian intermediate hosts. In the terrestrial environment, <i>T. gondii</i> prevalence increases with trophic level, consistent with predominant tissue cyst transmission. The highest prevalence was in terrestrial omnivores, which may reflect their synanthropic foraging behaviour. In aquatic species, prevalence was more consistent across trophic levels, but high prevalence in aquatic herbivores and insectivores reflects significant waterborne exposure to oocysts. Contrary to our predictions, generalized scavenging <i>per se</i> was not associated with increased prevalence.</p> <p><b>Main conclusions:</b> This study highlights the value of comparing pathogen prevalence among multiple ecological guilds and ecosystem types for a comprehensive understanding of the epidemiology of generalist pathogens, such as <i>T. gondii</i>. Increased effort is needed to reduce <i>T. gondii</i> spillover from the domestic cat cycle into wildlife populations.</p>
FIGURE. Thalictrum uncatum in the wild (Shangri-la in northwestern Yunnan, China). A. Habitat. B. Habit. C. Leaf (left: adaxial side; right: abaxial side). D. Leaflet (left: adaxial side; right: abaxial side). E. Flower. F. Sepals. G. Stamens. H. Carpels. I. Aggregate fruit (immature). J. Achenes (immature). Photographed by Y.P. Zeng. in Thalictrum spiristylum (Ranunculaceae), described from northwestern Yunnan, China, is merged with T. atriplex
FIGURE. Thalictrum uncatum in the wild (Shangri-la in northwestern Yunnan, China). A. Habitat. B. Habit. C. Leaf (left: adaxial side; right: abaxial side). D. Leaflet (left: adaxial side; right: abaxial side). E. Flower. F. Sepals. G. Stamens. H. Carpels. I. Aggregate fruit (immature). J. Achenes (immature). Photographed by Y.P. Zeng.
FIGURE. Thalictrum uncatum in the wild (Xiaojin county in western Sichuan, China). A. Habitat. B. Habit. C. Leaf (left: adaxial side; right: abaxial side). D. Leaflet (left: adaxial side; right: abaxial side). E. Portion of inflorescence. F. Flower. G. Sepals. H. Stamens. I. Carpels. J. Aggregate fruit (immature). K. Achenes (immature). Photographed by Y.P. Zeng. in Thalictrum spiristylum (Ranunculaceae), described from northwestern Yunnan, China, is merged with T. atriplex
FIGURE. Thalictrum uncatum in the wild (Xiaojin county in western Sichuan, China). A. Habitat. B. Habit. C. Leaf (left: adaxial side; right: abaxial side). D. Leaflet (left: adaxial side; right: abaxial side). E. Portion of inflorescence. F. Flower. G. Sepals. H. Stamens. I. Carpels. J. Aggregate fruit (immature). K. Achenes (immature). Photographed by Y.P. Zeng.
FIGURE. Thalictrum atriplex in the wild (Shangri-la county in northwestern Yunnan, China). A. Habitat. B. Habit. C. Roots. D. Portion of stem. E. Leaf (left: adaxial side; right: abaxial side). F. Leaflet (adaxial side). G. Portion of inflorescence. H. Flower. I. Sepal (left: adaxial side; right: abaxial side). J. Stamens. K. Carpels. L. Portion of infructescence. M. Aggregate fruits (immature). N. Achenes (immature). Photographed by Y.P. Zeng. in Thalictrum spiristylum (Ranunculaceae), described from northwestern Yunnan, China, is merged with T. atriplex
FIGURE. Thalictrum atriplex in the wild (Shangri-la county in northwestern Yunnan, China). A. Habitat. B. Habit. C. Roots. D. Portion of stem. E. Leaf (left: adaxial side; right: abaxial side). F. Leaflet (adaxial side). G. Portion of inflorescence. H. Flower. I. Sepal (left: adaxial side; right: abaxial side). J. Stamens. K. Carpels. L. Portion of infructescence. M. Aggregate fruits (immature). N. Achenes (immature). Photographed by Y.P. Zeng.
FIGURE. Thalictrum atriplex in the wild (Kangding county in western Sichuan, China, the type locality). A. Habitat. B. Habit. C. Roots. D. Portion of stem. E. Leaf (left: adaxial side; right: abaxial side). F. Leaflet (adaxial side). G. Portion of inflorescence. H. Flower. I. Sepal (left: adaxial side; right: abaxial side). J. Stamens. K. Carpels. L. Aggregate fruits (immature). M. Achenes (immature). Photographed by Y.P. Zeng. in Thalictrum spiristylum (Ranunculaceae), described from northwestern Yunnan, China, is merged with T. atriplex
FIGURE. Thalictrum atriplex in the wild (Kangding county in western Sichuan, China, the type locality). A. Habitat. B. Habit. C. Roots. D. Portion of stem. E. Leaf (left: adaxial side; right: abaxial side). F. Leaflet (adaxial side). G. Portion of inflorescence. H. Flower. I. Sepal (left: adaxial side; right: abaxial side). J. Stamens. K. Carpels. L. Aggregate fruits (immature). M. Achenes (immature). Photographed by Y.P. Zeng.
FIGURE. Thalictrum spiristylum (= T. atriplex) in the wild (Ninglang county in northwestern Yunnan, China). A. Habitat. B. Habit (flowering plant). C. Habit (fruiting plant). D. Roots. E. Portion of stem. F. Leaf (left: adaxial side; right: abaxial side). G. Leaflet (adaxial side). H. Portion of inflorescence. I. Flower. J. Sepals (adaxial side). K. Stamens. L. Carpels. M. Portion of infructescence. N. Aggregate fruits (immature). O. Achenes (immature). Photographed by Y.P. Zeng. in Thalictrum spiristylum (Ranunculaceae), described from northwestern Yunnan, China, is merged with T. atriplex
FIGURE. Thalictrum spiristylum (= T. atriplex) in the wild (Ninglang county in northwestern Yunnan, China). A. Habitat. B. Habit (flowering plant). C. Habit (fruiting plant). D. Roots. E. Portion of stem. F. Leaf (left: adaxial side; right: abaxial side). G. Leaflet (adaxial side). H. Portion of inflorescence. I. Flower. J. Sepals (adaxial side). K. Stamens. L. Carpels. M. Portion of infructescence. N. Aggregate fruits (immature). O. Achenes (immature). Photographed by Y.P. Zeng.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.