cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp3/r5zafw
title: Adaptation across geographic ranges is consistent with strong selection in marginal climates and legacies of range expansion

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Every species experiences limits to its geographic distribution. Some evolutionary models predict that populations at range edges are less well-adapted to their local environments due to drift, expansion load, or swamping gene flow from the range interior. Alternatively, populations near range edges might be uniquely adapted to marginal environments. In this study, we use a database of transplant studies that quantify performance at broad geographic scales to test how local adaptation, site quality, and population quality change from spatial and climatic range centers towards edges. We find that populations from poleward edges perform relatively poorly, both on average across sites (15% lower population quality) and when compared to other populations at home (31% relative fitness disadvantage), consistent with these populations harboring high genetic load. Populations from equatorial edges also perform poorly on average (18% lower population quality) but, in contrast, outperform foreign populations (16% relative fitness advantage), suggesting that populations from equatorial edges have adapted to unique environments. Finally, we find that populations from sites that are thermally extreme relative to the species' niche demonstrate strong local adaptation, regardless of geographic position. Our findings indicate that both nonadaptive processes and adaptive evolution contribute to variation in adaptation across species' ranges.
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;This dataset contains fitness data gathered from a systematic literature search of transplant experiments, along with geographic and climatic covariates derived for this study. Included is the final data file and model running scripts, as well as scripts, GBIF occurrence data, and intermediate files demonstrating how spatial and climatic predictors were calculated.&lt;/p&gt;
description: &lt;b&gt;Usage notes&lt;/b&gt;&lt;br /&gt;&lt;p&gt;See README file.&lt;/p&gt;
description: <b>Dryad version number:</b> 3
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.pnvx0k6mc
<b>Storage size:</b> 84158501
<b>Visibility:</b> public
DOI: 10.5683/sp3/tl6kbt
title: Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Parallel evolution of lateral plates and body shape in threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence and whole-body phenotypes to determine genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment and we provide an example of the genetic basis for parallel evolutionon a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population are not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.&lt;/p&gt;
description: <b>Dryad version number:</b> 1
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.g79cnp5wz
<b>Storage size:</b> 873737
<b>Visibility:</b> public
DOI: 10.5683/sp3/iie5pr
title: Chicken and junglefowl cerebellar anatomy data

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Domestication is the process by which wild organisms become adapted for human use. Many phenotypic changes are associated with animal domestication, including decreases in brain and brain region sizes. In contrast to this pattern, the chicken has a larger cerebellum compared with the wild red junglefowl, but what neuroanatomical changes are responsible for this difference have yet to be investigated. Here, we quantified cell layer volumes, neuron numbers and neuron sizes in the cerebella of chickens and junglefowl. Chickens have larger, more folded cerebella with more and larger granule cells than junglefowl, but neuron numbers and cerebellar folding were proportional to cerebellum size. However, chickens do have relatively larger granule cell layer volumes and relatively larger granule cells than junglefowl. Thus, the chicken cerebellum can be considered a scaled-up version of the junglefowl cerebellum, but with enlarged granule cells. The combination of scaling neuron number and disproportionate enlargement of cell bodies partially supports a recent theory that domestication does not affect neuronal density within brain regions. Whether the neuroanatomical changes we observed are typical of domestication or not requires similar quantitative analyses in other domesticated species and across multiple brain regions.&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;All of the data was collected from histological sections using unbiased stereology as outlined in the accompanying manuscript.&lt;/p&gt;
description: <b>Dryad version number:</b> 2
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.hhmgqnkhj
<b>Storage size:</b> 31297
<b>Visibility:</b> public
DOI: 10.5683/sp3/yofeir
title: Chimpanzees use least-cost routes to out-of-sight goals

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;While the ability of naturally ranging animals to recall the location of food resources and use straight-line routes between them has been demonstrated in several studies [1, 2], it is not known whether animals can use knowledge of their landscape to walk least-cost routes [3]. This ability is likely to be particularly important for animals living in highly variable energy landscapes, where movement costs are exacerbated [4, 5].  Here, we used least-cost modelling, which determines the most efficient route assuming full knowledge of the environment, to investigate whether chimpanzees (Pan troglodytes) living in a rugged, montane environment walk least-cost routes to out of sight goals. We compared the ‘costs’ and geometry of observed movements with predicted least-cost routes and local knowledge (agent-based) and straight-line null models.  The least-cost model performed better than the local knowledge and straight-line models across all parameters, and linear mixed modelling showed a strong relationship between the cost of observed chimpanzee travel and least-cost routes.  Our study provides the first example of the ability to take least-cost routes to out of sight goals by chimpanzees and suggests they have spatial memory of their home range landscape. This ability may be a key trait that has enabled chimpanzees to maintain their energy balance in a low-resource environment.  Our findings provide a further example of how the advanced cognitive complexity of hominins may have facilitated their adaptation to a variety of environmental conditions and lead us to hypothesise that landscape complexity may play a role in shaping cognition.&lt;/p&gt;
description: <b>Dryad version number:</b> 3
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.wdbrv15m7
<b>Storage size:</b> 68819
<b>Visibility:</b> public
DOI: 10.5683/sp3/dy8zoe
title: Coevolution of relative brain size and life expectancy in parrots

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p style="text-align:start;text-indent:0px;"&gt;&lt;span style="font-style:normal;"&gt;&lt;span style="font-weight:normal;"&gt;&lt;span style="letter-spacing:normal;"&gt;&lt;span style="white-space:normal;"&gt;Previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa. Little research has been devoted to understanding this link in parrots; yet parrots are well-known for both their exceptionally long lives and cognitive complexity. We employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on longevity in parrots. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the &lt;em&gt;Cognitive Buffer Hypothesis&lt;/em&gt;, which proposes that increased cognitive abilities enable longer life spans, and the &lt;em&gt;Expensive Brain Hypothesis&lt;/em&gt;, which holds that increases in life span are caused by prolonged developmental time of, and increased parental investment in, large-brained offspring&lt;em&gt;. &lt;/em&gt;We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using a principled Bayesian approach that addresses data uncertainty and imputation of missing values, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction. Our results suggest that selection for enhanced cognitive abilities in parrots have in turn promoted longer lifespans.&lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;Data was collected from zoo records (Species360 ZIMS, with permission), museum specimens and from the litterture. Data has been processed with bespoke Bayesian models. Raw data is avaible when possible (some data is sensitive). Intermediate data and final results are available. Code is available. &lt;/p&gt;
description: &lt;b&gt;Usage notes&lt;/b&gt;&lt;br /&gt;&lt;p&gt;Readme's are included with instruction on how to reproduce the steps. &lt;/p&gt;
description: <b>Dryad version number:</b> 5
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.sbcc2fr7x
<b>Storage size:</b> 662067266
<b>Visibility:</b> public
DOI: 10.5683/sp3/ofdlmf
title: Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Three distinct Canada jay (&lt;em&gt;Perisoreus canadensis&lt;/em&gt;) morphotypes with easily recognizable plumage traits come into contact in western North America. Recent work demonstrated high genetic structure across the species’ range; however, patterns of genetic variation in these contact zones remain unknown. We categorized 605 individuals into one of three morphotypes (Pacific, Rocky Mountain, and Boreal) based on plumage, and genotyped individuals at the mtDNA control region and 12 microsatellite loci to assess the extent of hybridization between morphotypes. Our data showed cryptic genetic diversity and high cytonuclear discordance among morphotypes within contact zones, which is likely the result of recent and historical admixture. The distributions of the Boreal and Pacific morphotypes each showed a strong association with a single, distinct genetic group, whereas the Rocky Mountain morphotype exhibited higher genetic diversity and was associated with multiple genotypes. Our analyses show the importance of considering both plumage and genetic traits when examining contact zones between closely related taxa. Finally, the data presented in this study reaffirm that the Pacific morphotype is distinct from the Boreal and Rocky Mountain morphotypes based on genetic, phenotypic, and ecological data, indicating that the Pacific morphotype should be re-elevated to a full species.&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;This file contains microsatellite genotyping data, as well as morphotype and mtDNA clade information. &lt;/p&gt;
description: <b>Dryad version number:</b> 4
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.ht76hdrdq
<b>Storage size:</b> 464768
<b>Visibility:</b> public
DOI: 10.5683/sp3/avvo1r
title: Data for: Caloric restriction extends lifespan in a clonal plant

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;When subjected to dietary caloric restriction (CR), individual animals often outlive well-fed conspecifics. Here, we address whether CR also extends lifespan in plants. Whereas caloric intake in animals comes from ingestion, in plants it derives from photosynthesis. Thus, factors that reduce photosynthesis, such as reduced light intensity, can induce CR. In two lab experiments investigating the aquatic macrophyte &lt;em&gt;Lemna minor&lt;/em&gt;, we tracked hundreds of individuals longitudinally, with light intensity – and hence, CR – manipulated using neutral-density filters. In both experiments, CR dramatically increased lifespan through a process of temporal scaling. Moreover, the magnitude of lifespan extension accorded with the assumptions that (a) light intensity positively relates to photosynthesis following Michaelis-Menten kinetics, and (b) photosynthesis negatively relates to lifespan via a power law. Our results emphasize that CR-mediated lifespan extension applies to autotrophs as well as heterotrophs, and suggest that variation in light intensity has quantitatively predictable effects on plant aging trajectories.&lt;/p&gt;
description: <b>Dryad version number:</b> 7
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.4qrfj6qgz
<b>Storage size:</b> 181653
<b>Visibility:</b> public
DOI: 10.5683/sp3/tu7vhz
title: Data for: Effects of parental age on salt stress tolerance in an aquatic plant

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Parental age influences components of offspring fitness in many species. The ability to tolerate stress also affects fitness, but less is known regarding changes in offspring stress tolerance with increasing parental age, especially in plants. We examined first and fifth-born clonal offspring (using birth order as a proxy for parental age), and compared their fitness in several sub-lethal concentrations of salt (NaCl), to investigate the interactive effects of birth order and salt stress on the offspring of the aquatic plant &lt;em&gt;Lemna minor &lt;/em&gt;L. We found that increasing salt concentration reduced reproduction particularly at early ages, which detrimentally affected fitness, as measured by the intrinsic rate of natural increase. Fifth offspring had greater fitness than first offspring, potentially due to the hump-shaped relationship between offspring fitness and birth order observed in other studies on &lt;em&gt;Lemna&lt;/em&gt;, with fifth offspring near the peak of the hump. We found no interactive effect of birth order and salt concentration on offspring fitness; however, there were interactive effects on the time to first reproduction and the size of fronds. Specifically, first offspring exposed to increasing salt concentrations exhibited longer delays to first reproduction and grew to a greater size, while fifth offspring showed little change in either variable with increasing salt concentration. Thus, variation in birth order affected offspring response to salt stress, although not in terms of fitness. These results help illuminate factors impacting the age-specific strength of natural selection and stress responses, and may be environmentally relevant in the context of environmental salinization.&lt;/p&gt;
description: &lt;b&gt;Usage notes&lt;/b&gt;&lt;br /&gt;&lt;p&gt;R software is required to run the script.&lt;/p&gt;
description: <b>Dryad version number:</b> 2
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.wpzgmsbr6
<b>Storage size:</b> 173498
<b>Visibility:</b> public
DOI: 10.5683/sp3/xzpajc
title: Data for: Inhibition is a prevalent mode of activity in the neocortex around awake hippocampal ripples in mice

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Coordinated peri-ripple activity in the hippocampal-neocortical network is essential for mnemonic information processing in the brain. Hippocampal ripples likely serve different functions in sleep and awake states. Thus, the corresponding neocortical activity patterns may differ in important ways. We addressed this possibility by conducting voltage and glutamate wide-field imaging of the neocortex with concurrent hippocampal electrophysiology in awake mice. Contrary to our previously published sleep results, deactivation and activation were dominant in post-ripple neocortical voltage and glutamate activity, respectively, especially in the agranular retrosplenial cortex (aRSC). Additionally, the spiking activity of aRSC neurons, estimated by two-photon calcium imaging, revealed the existence of two subpopulations of excitatory neurons with opposite peri-ripple modulation patterns: one increases and the other decreases firing rate. These differences in peri-ripple spatiotemporal patterns of neocortical activity in sleep versus awake states might underlie the reported differences in the function of sleep versus awake ripples.&lt;/p&gt;
description: &lt;b&gt;Usage notes&lt;/b&gt;&lt;br /&gt;&lt;p&gt;This dataset could be opened in MATLAB. &lt;/p&gt;
&lt;p&gt;The VSFP and iGluSnFR datasets are organized in matrices whose dimensions correspond to ripple by time (1 second before and after ripple centers).&lt;/p&gt;
&lt;p&gt;The calcium and deconvolved traces in 2P calcium dataset are organized in neuron by time (3 seconds before and after ripple centers) by ripples format. &lt;/p&gt;
&lt;p&gt;For the VSFP datasets, the imaging and electrophysiology sampling rates are 100 and 2000 Hz, respectively. &lt;/p&gt;
&lt;p&gt;For the iGluSnFR dataset, the imaging and electrophysiology sampling rates are 100 and 1000 Hz, respectively. &lt;/p&gt;
&lt;p&gt;For the 2P calcium dataset, the imaging and electrophysiology sampling rates are reported inside the dataset's file. &lt;/p&gt;
&lt;p&gt;For ROI names, please refer to &lt;a href="https://doi.org/10.7554/eLife.51972" target="_blank" rel="noopener"&gt;https://doi.org/10.7554/eLife.51972&lt;/a&gt;.&lt;/p&gt;
description: <b>Dryad version number:</b> 6
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.8kprr4xrk
<b>Storage size:</b> 2370851243
<b>Visibility:</b> public
DOI: 10.5683/sp3/a4ztd7
title: Data for: Non-host species reduce parasite infection in a focal host species within experimental fish communities

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p class="MsoCommentText"&gt;The dilution effect describes the negative association between host biodiversity and the risk of infectious disease. Tests designed to understand the relative roles of host species richness, host species identity, and rates of exposure within experimental host communities would help resolve ongoing contention regarding the importance and generality of dilution effects. We exposed fathead minnows to infective larvae of the trematode, &lt;i&gt;Ornithodiplostomum ptychocheilus &lt;/i&gt;in minnow-only containers and in mixed containers that held 1-3 other species of fish. Parasite infection was estimated as the numbers of encysted worms (i.e., brainworms) present in minnows following exposure. The results of exposure trials showed that non-minnow fish species were incompatible with &lt;i&gt;O. ptychocheilus&lt;/i&gt; larvae. There was no reduction in mean brainworm counts in minnows in mixed containers with brook sticklebacks or longnose dace. In contrast, brainworm counts in minnows declined by 51% and 27% in mesocosms and aquaria, respectively, when they co-occurred with emerald shiners. Dilution within minnow + shiner containers may arise from shiner-induced alterations in minnow or parasite behaviours that reduced encounter rates between minnows and parasite larvae. Alternatively, shiners may act as parasite sinks for parasite larvae. These results highlight the role of host-species identity in the dilution effect. Our results also emphasize the complex and idiosyncratic effects of host community composition on rates of parasite infection within contemporary host communities that contain combinations of introduced and native species.&lt;/p&gt;
description: <b>Dryad version number:</b> 5
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.0p2ngf21r
<b>Storage size:</b> 113406
<b>Visibility:</b> public
DOI: 10.5683/sp3/qtqdvu
title: Data for: Strong effects of food quality on host life history do not scale to impact parasitoid efficacy or life history

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;span lang="EN-US"&gt;Parasitoids are small insects, (e.g., small wasps or flies) that reproduce by laying eggs on or within host arthropods. Parasitoids make up a large proportion of the world’s biodiversity and are popular agents of biological control. Idiobiont parasitoids paralyze their hosts upon attack and thus are expected to only target hosts large enough to support offspring development. Host resources generally impact host attributes and life histories including size, development, and life span. Some argue slow host development in response to resource quality increases parasitoid efficacy (i.e., a parasitoid’s ability to successfully reproduce on or within a host) due to longer host exposure to parasitoids. However, this hypothesis is not always supported and does not consider variation in other host traits in response to resources that may be important for parasitoids (e.g., variation in host size is known to impact parasitoid efficacy). In this study, we test whether trait variation within host developmental stages in response to host resources is more important for parasitoid efficacy and life histories than trait variation across host developmental stages. We exposed seed beetle hosts raised on a food quality gradient to mated female parasitoids and measured the number of hosts parasitized and parasitoid life history traits at the scale of host stage- and age-structure. Our results suggest host food quality does not cascade to impact idiobiont parasitoid life histories despite large food quality effects on host life history. Instead, variation in host life histories across host developmental stages better predicts parasitoid efficacy and life histories, suggesting finding a host in a specific instar is more important for idiobiont parasitoids than finding hosts on or within higher quality resources.&lt;/span&gt;&lt;/p&gt;
description: <b>Dryad version number:</b> 6
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/stash/dataset/doi:10.5061/dryad.3ffbg79n3
<b>Storage size:</b> 1077690
<b>Visibility:</b> public