cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0438741
title: Weak local adaptation to drought in seedlings of a widespread conifer

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Tree seedlings from populations native to drier regions are often assumed to be more drought tolerant than those from wetter provenances. However, intraspecific variation in drought tolerance has not been well characterized despite being critical for developing climate change mitigation and adaptation strategies, and for predicting the effects of drought on forests.&lt;/p&gt; &lt;p&gt;We used a large-scale common-garden drought-to-death experiment to assess range-wide variation in drought tolerance measured by decline of photosynthetic efficiency, growth, and plastic responses to extreme summer drought in seedlings of 73 natural populations of the two main varieties of Douglas-fir (&lt;em&gt;Pseudotsuga menziesii &lt;/em&gt;var. &lt;em&gt;menziesii &lt;/em&gt;and var. &lt;em&gt;glauca&lt;/em&gt;).&lt;/p&gt; &lt;p&gt;Local adaptation to drought was weak in var. &lt;em&gt;glauca &lt;/em&gt;and nearly absent in &lt;em&gt;menziesii.&lt;/em&gt; Var. &lt;em&gt;glauca&lt;/em&gt; showed higher tolerance to drought but slower growth than var. &lt;em&gt;menziesii&lt;/em&gt;. Clinal variation in drought tolerance and growth species-wide was mainly associated with temperature rather than precipitation. A higher degree of plasticity for growth was observed in var. &lt;em&gt;menziesii&lt;/em&gt; in response to extreme drought.&lt;/p&gt; &lt;p&gt;Genetic variation for drought tolerance in seedlings within varieties is maintained primarily within populations. Selective breeding within populations may facilitate adaptation to drought more than assisted gene flow.&lt;/p&gt;
DOI: 10.14288/1.0438757
title: Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome—for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA—show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (&lt;em&gt;Zonotrichia atricapilla&lt;/em&gt;) and the white-crowned sparrow (&lt;em&gt;Zonotrichia leucophrys&lt;/em&gt;) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms (SNPs) to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of &lt;em&gt;Z. leucophrys&lt;/em&gt;. The two &lt;em&gt;Z. leucophrys&lt;/em&gt; subspecies showed moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species &lt;em&gt;Z. leucophrys&lt;/em&gt; and &lt;em&gt;Z. atricapilla&lt;/em&gt; show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between &lt;em&gt;Z. atricapilla&lt;/em&gt; and &lt;em&gt;Z. leucophrys&lt;/em&gt; appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria appear highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing lack of gene flow between populations many hundreds of thousands of years before other genomic regions.&lt;/p&gt;
DOI: 10.14288/1.0438904
title: High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p class="paragraph" style="line-height:150%;vertical-align:baseline;"&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, &lt;/span&gt;&lt;span class="normaltextrun"&gt;&lt;span lang="EN-GB" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;we developed a linkage map relying on 21,570 SNP makers in &lt;/span&gt;&lt;/span&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;Sitka spruce (&lt;em&gt;Picea sitchensis&lt;/em&gt; [Bong.] Carr.)&lt;/span&gt;&lt;span class="normaltextrun"&gt;&lt;em&gt;&lt;span lang="EN-GB" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;, &lt;/span&gt;&lt;/em&gt;&lt;/span&gt;&lt;span class="normaltextrun"&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. &lt;/span&gt;&lt;/span&gt;&lt;span lang="EN-US" style="font-size:11.0pt;line-height:150%;font-family:'Calibri' , sans-serif;"&gt;We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for &lt;em&gt;P. sitchensis&lt;/em&gt; and &lt;em&gt;P. glauca&lt;/em&gt; based on 27,052 makers and 11,609 gene sequences. Altogether, these two linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed herein opens new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.&lt;/span&gt;&lt;/p&gt;
DOI: 10.14288/1.0445426
title: Data used in the manuscript of "Wind and river effects on a coastal current in Chatham Sound, British Columbia"

description: Analytical data in support of the manuscript "Wind and river effects on a coastal current in Chatham Sound, British Columbia", which is submitted to Journal of Geophysical Research: Oceans. One could use the data to generate any figure in the manuscript. (2024-1-26)
DOI: 10.14288/1.0445026
title: DataSet for Effect of Flowrate, Tubing, and Incubation for DynaBeads Streptavidin with biotinylated BSA Droplets in Dual Phase Lab-in-Tubing Microfluidics

description: Droplets consisting of Dynabeads M-270, C1, T1 Streptavidin (Invitrogen) and 10 mg of VECTB2007 biotinylated bovine serum albumin (BSA) (Vector Laboratories) at 1.6µg/mL in dual-phase microfluidics at varying speeds 60, 90, and 120µL/min flowrate in two different types of tubing i.e. PTFE and Tygon. Non-biotinylated BSA in PBS buffer is used as the negative control. Images are extracted from the videos and cropped around the droplets. Droplets pass through three different viewing windows to show the effects of incubation.
DOI: 10.15468/dl.ak55j5
title: Occurrence Download

description: A dataset containing 155935 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((2.88987 50.07697,3.16544 50.00553,3.97172 49.85584,4.39017 50.54646,3.73018 51.19625,3.25389 51.27109,2.98173 51.26769,2.82132 51.17909,2.65513 51.16903,2.51915 51.04385,2.30853 50.74683,2.37956 50.2777,2.74968 50.10032,2.88987 50.07697))",
 "OccurrenceStatus is Present",
 "PublishingOrg is c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f",
 "TaxonKey is Aves",
 "Year 2015-2025"
 ]
}

 The dataset includes 155935 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000501-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0439408
title: Replication Data for: Early pain experiences in dairy calves on pain sensitivity later in life

description: In humans, early painful experiences can increase pain sensitivity later in life, but little is known regarding this phenomenon in cattle. This study assessed if a painful event early in life affects later pain sensitivity in 40-d-old calves. Holstein calves (n = 26) were randomly assigned to control or treatment conditions, blocked within sex and birth weight. At 9.5 ± 1.8 d old, treatment calves had 1 horn bud disbudded using caustic paste, whereas control calves had 1 horn sham disbudded; in both cases, multimodal pain control was provided. All calves had the contralateral horn bud disbudded using a hot iron 4 wk later, again with multimodal pain control. Mechani- cal nociceptive responses were assessed weekly using an algometer applied adjacent to both horn buds and on the rump, beginning 3 d before the first disbudding and ending 30 d after the second disbudding. Following the second disbudding, both groups of calves showed evidence of increased sensitivity (i.e., algometer pressure declined 3.69 ± 0.60 √N to 2.13 ± 0.70 √N) on the contralateral bud, but there was no difference between the control group and the treatment groups. An interaction between treatment and time, likely driven by treatment differences, was found on the rump when tested 5 h after the second disbudding event. These responses are not consistent with the hypothesis that an early pain experience results in increased sensitivity to later painful experiences.
DOI: 10.14288/1.0439026
title: Open data webinar: Revolutionizing clinical research - Exploring open data initiatives for innovation and impact

description: "Revolutionizing clinical research: Exploring open data initiatives for innovation and impact" an open data webinar hosted by the Pediatric Sepsis Data CoLaboratory.&lt;br /&gt; &lt;br /&gt;Given how pervasive (and complex) Artificial Intelligence (AI) I is going to be, it is unlikely that a few organizations can truly regulate the technology. Its oversight will require everyone pitching in. That, in turn, requires everyone having some basic understanding of how AI is developed, and more importantly, the risks associated with its use. But how do we build capacity in a field that is moving at warped speed? There will be no individual experts in the field, only collective wisdom. Legacy education and knowledge systems are too inflexible and siloed to keep up with the science and understand the sociology of AI. Datathons are designed to operationalize the multi-disciplinary hive learning that addresses the challenges of AI education and training. In this webinar, speakers discuss data bias and AI and their experience with optimizing reuse of data to advance health research through Datathons.&lt;br /&gt; &lt;br /&gt;&lt;strong&gt;Presenters:&lt;/strong&gt; &lt;br /&gt;1. "What's the Fuss about Artificial Intelligence (AI)?" - Speaker: Leo Anthony Celi, Principal Research Scientist, Massachusetts Institute of Technology; Associate Professor of Medicine, Harvard Medical School; Editor-in-Chief, PLOS Digital Health.&lt;br /&gt; &lt;br /&gt;2. "SATI-Q Program: 20 Years of History in Quality Benchmarking, Evolution and Future Perspectives" - Speaker: Ariel Leonardo Fernández, Software Developer, Quality Benchmarking Program (SATI-Q), Argentina Society of Intensive Care (SATI). &lt;br /&gt; &lt;br /&gt;&lt;strong&gt;Data Description:&lt;/strong&gt; Presentation slides, webinar video - Full (55m), webinar video - Celi (21m), webinar video - Fernández (13m). &lt;br /&gt;
DOI: 10.14288/1.0439349
title: Replication Data for: Effect of social relationships on dairy cows’ decision to move to and from an outdoor area.

description: Leader-follower behaviours have been described in cattle housed on pasture and when entering the milking parlour. To our knowledge, no study has investigated these behaviours in cattle provided free-choice access to the outdoors. This study explores whether the timing of cows exiting and entering the barn from an outdoor area is associated with the movement of their herd mates. We followed 18 lactating Holstein cows housed indoors in a freestall barn together with 18 non-experimental cows, for on average 77 d (range: 74 – 80). The 18 experimental cows were allowed free access to an outdoor open pack (sand covered with woodchips) through an automated selection gate which automatically recorded when a cow exited the barn. To enter the barn from outside, cows went through a one-way gate; time of entry was recorded from video. Cows moved in and out of the barn on average 269 times (range: 68 – 472). A Gaussian mixture model was applied to the log of the frequency distribution of time intervals between each cow and the next for each entry and exit. On the basis of where the curves intersected, we identified a threshold interval of 42 s between consecutive exits or entries to consider movements as associated. Applying this threshold, 13.8 % of events were associated with the movement of another cow: 11.2 % of exits and 16.4 % of entries. We created a leader-follower matrix for each direction: the leader being the cow initiating the movement, and the follower the one walking through the same gate within 42 s of the leader. These association matrices were used to build weighted and directed social networks for exits and entries; we found a moderate positive correlation between the networks (RQAP = 0.69, p &lt; 0.001), meaning the patterns of association between cows observed when exiting the barn were consistent with those when they entered. Just over a third of the relations in the networks were asymmetrical; in contrast, leader-follower theory would predict that one individual within each pair would lead consistently. We identified 17 of 153 possible between-cow pairings as preferentially bonded; these pairs had a simple ratio index of association more than twice the average of all possible pairs. We conclude that some of the cow movements to and from an outdoor pack were influenced by the movements of other group members, and these associations were particularly strong between some pairs of cows.
DOI: 10.14288/1.0439652
title: Heatwave-mediated decreases in phytoplankton quality negatively affect zooplankton productivity

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;ol&gt; &lt;li&gt;Climate change is expected to increase the frequency of extreme temperature events. The effect of heatwaves on phytoplankton is of particular concern because they are a key source of C, N, P, and essential fatty acids to aquatic ecosystems. Laboratory studies have demonstrated that phytoplankton grown at warmer temperatures are a lower-quality food source, but how heatwaves affect phytoplankton quality at the community scale is currently unclear.&lt;/li&gt; &lt;li&gt;Here we address this knowledge gap by growing natural assemblages of freshwater phytoplankton at ‘ambient’, ‘constant warming’, or ‘heatwave’ conditions. We next fed these phytoplankton communities to natural assemblages of zooplankton to test the prediction that zooplankton that consume heatwave-exposed phytoplankton will exhibit reductions in biomass.&lt;/li&gt; &lt;li&gt;Our experiment demonstrated that zooplankton that consumed ‘heatwave’ phytoplankton attained lower community biomass than those fed ‘constant warming’ or ‘ambient’ phytoplankton. Additionally, despite receiving similar total heat input, phytoplankton exposed to ‘heatwave’ conditions contained lower C, N, P, and fatty acid concentrations compare to phytoplankton grown in ‘constant warming’ conditions.&lt;/li&gt; &lt;li&gt;Correlations between zooplankton biomass and all measured phytoplankton traits revealed that decreases in zooplankton biomass were best explained by low quantities of C, N, and monounsaturated fatty acids in ‘heatwave’ phytoplankton.&lt;/li&gt; &lt;li&gt;Our study demonstrates that the effects of heatwaves on phytoplankton quality are clearly distinct from those caused by constant warming temperatures, and that heatwave-mediated decreases in resource quality have immediate effects on consumer productivity. &lt;/li&gt; &lt;/ol&gt;
DOI: 10.14288/1.0439958
title: Trophic cascade within and across ecosystems: the role of anti-predatory defenses, predator type, and detritus quality

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;ol&gt; &lt;li&gt;Species in one ecosystem can indirectly affect multiple biodiversity components and ecosystem functions of adjacent ecosystems. The magnitude of these cross-ecosystem effects depends on the attributes of the organisms involved in the interactions, including traits of the predator, prey and basal resource. However, it is unclear how predators with cross-ecosystem habitat interact with predators with single-ecosystem habitat to affect their shared ecosystem. Also, unknown is how such complex top-down effects may be mediated by the anti-predatory traits of prey and quality of the basal resource.&lt;/li&gt; &lt;li&gt;We used the aquatic invertebrate food webs in tank bromeliads as a model system to investigate these questions. We manipulated the presence of a strictly aquatic predator (damselfly larvae) and a predator with both terrestrial and aquatic habitats (spider) and examined effects on survival of prey (detritivores grouped by anti-predator defense), detrital decomposition (of two plant species differing in litter quality), nitrogen flux and host plant growth. To evaluate the direct and indirect effects of each predator type on multiple detritivore groups and ultimately on multiple ecosystem processes, we used piecewise structural equation models. For each response variable, we isolated the contribution of different detritivore groups to overall effects by comparing alternate model formulations.&lt;/li&gt; &lt;li&gt;Alone, damselfly larvae and spiders each directly decreased survival of detritivores and caused multiple indirect negative effects on detritus decomposition, nutrient cycling, and host plant growth. However, when predators co-occurred, the spider caused a negative non-consumptive effect on the damselfly larva, diminishing the net direct and indirect top-down effects on the aquatic detritivore community and ecosystem functioning. Both detritivore traits and detritus quality modulated the strength and mechanism of these trophic cascades. Predator interference was mediated by undefended or partially defended detritivores as detritivores with anti-predatory defenses evaded consumption by damselfly larvae but not spiders. Predators and detritivores affected ecosystem decomposition and nutrient cycling only in the presence of high-quality detritus, as the low-quality detritus was consumed more by microbes than invertebrates.&lt;/li&gt; &lt;li&gt;The complex responses of this system to predators from both recipient and adjacent ecosystems highlight the critical role of maintaining biodiversity components across multiple ecosystems. &lt;/li&gt; &lt;/ol&gt;
DOI: 10.14288/1.0439959
title: Dataset of how animal movement paths in a landscape vary due to wildfire

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Animals navigate landscapes based on perceived risks vs. rewards, as inferred from features of the landscape. In the wild, knowing how strongly animal movement is directed by landscape features is difficult to ascertain, but widespread disturbances such as wildfires can serve as natural experiments. We tested the hypothesis that wildfires homogenize the risk/reward landscape, causing movement to become less directed, given that fires reduce landscape complexity as habitat structures (e.g., tree cover, dense brush) are burned&lt;em&gt;. &lt;/em&gt;We used satellite imagery of a research reserve in Northern California to count and categorize paths made primarily by mule deer (&lt;em&gt;Odocoileus hemionus&lt;/em&gt;) in grasslands. Specifically, we compared pre-wildfire (August 2014) and post-wildfire (September 2018) image history layers among locations that were or were not impacted by wildfire (i.e., a Before/After Control/Impact design). Wildfire significantly altered spatial patterns of deer movement: more new paths were gained and more old paths were lost in areas of the reserve that were impacted by wildfire; movement patterns became less directed in response to fire, suggesting that the risk/reward landscape became more homogenous, as hypothesized. We found evidence to suggest that wildfire affects deer populations at spatial scales beyond their scale of direct impact and raises the interesting possibility that deer perceive risks and rewards at different spatial scales. In conclusion, our study provides an example of how animals integrate spatial information from the environment to make movement decisions, setting the stage for future work on the broader ecological implications for populations, communities, and ecosystems, an emerging interest in ecology.&lt;/p&gt;
DOI: 10.14288/1.0439960
title: Data from: Manipulation of soil mycorrhizal fungi Influences floral display traits

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Most plants form root hyphal relationships with mycorrhizal fungi, especially arbuscular mycorrhizal fungi (AMF). These associations are known to positively impact plant biomass and competitive ability. However, less is known about how mycorrhizae may impact other ecological interactions, such as those mediated by pollinators.&lt;/p&gt; &lt;p&gt;We performed a meta-regression of studies that manipulated AMF and measured traits related to pollination, including floral display, rewards, visitation, and reproduction, extracting 63 studies with 423 effects.&lt;/p&gt; &lt;p&gt;On average, the presence of mycorrhizae was associated with positive effects on floral traits. Specifically, we found impacts of AMF on floral display, pollinator visitation and reproduction, and a positive but non-significant impact on rewards. Studies manipulating mycorrhizae with fungicide tended to report contrasting results, possibly because fungicide destroys both beneficial and pathogenic microbes.&lt;/p&gt; &lt;p&gt;Our study highlights the potential for relationships with mycorrhizal fungi to play an important, yet underrecognized role in plant-pollinator interactions. With heightened awareness of the need for a more sustainable agricultural industry, mycorrhizal fungi may offer the opportunity to reduce reliance on inorganic fertilizers. At the same time, fungicides are now ubiquitous in agricultural systems. Our study demonstrates indirect ways in which plant-belowground fungal partnerships could manifest in plant-pollinator interactions.&lt;/p&gt;