cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0398088
title: Data from: Recently-formed polyploid plants diversify at lower rates

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macro-evolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead-end, whereas recent genomic studies suggest that polyploidy has been a key driver of macro-evolutionary success. Here we examine the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly “fit” lineages of polyploids may persist to enjoy longer term evolutionary success.
DOI: 10.14288/1.0398091
title: Data from: Too much of a good thing: The unique and repeated paths toward copper adaptation

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Copper is a micronutrient essential for growth due to its role as a co-factor in enzymes involved in respiration, defense against oxidative damage, and iron uptake. Yet too much of a good thing can be lethal, and yeast cells typically do not have tolerance to copper levels much beyond the concentration in their ancestral environment. Here, we report a short-term evolutionary study of Saccharomyces cerevisiae exposed to levels of copper sulfate that are inhibitory to the initial strain. We isolated and identified adaptive mutations soon after they arose, reducing the number of neutral mutations, to determine the first genetic steps that yeast take when adapting to copper. We analyzed 34 such strains through whole-genome sequencing and by assaying fitness within different environments; we also isolated a subset of mutations through tetrad analysis of four lines. We identified a multi-layered evolutionary response. In total, 57 single base-pair mutations were identified across the 34 lines. In addition, gene amplification of the copper metallothionein protein, CUP1, was rampant, as was chromosomal aneuploidy. Four other genes received multiple, independent mutations in different lines (the vacuolar transporter genes VTC1 and VTC4; the plasma membrane H+-ATPase PMA1; and MAM3, a protein required for normal mitochondrial morphology). Analyses indicated that mutations in all four genes, as well as CUP1 copy number, contributed significantly to explaining variation in copper tolerance. Our study thus finds that evolution takes both common and less trodden pathways toward evolving tolerance to an essential, but highly toxic, micronutrient.
DOI: 10.14288/1.0398094
title: Data from: The conservation value of high elevation habitats to North American migrant birds

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The basic patterns of faunal community composition and habitat associations of high elevation mountainous regions are poorly-known. This is true for the avifauna of western North America where our knowledge of high elevation use is primarily restricted to breeding assemblages. Here we report on systematic avian surveys of high elevation habitats over four years in British Columbia conducted during the post-breeding and fall migration periods (Aug–Oct). We detected a remarkable diversity of birds (95 species in 30 families) using alpine, subalpine, and montane forest, many of which used these habitats seasonally. One quarter of the species are on lists of conservation concern. Density, species richness, and community composition varied considerably between habitats and mountain ranges within the study area, especially between the western slope of the Coast range and other ranges. Most species exhibited strong temporal variation in patterns of abundance that were related to migratory behavior. From an extensive literature-based survey, we found that ~ 35% of North America's breeding bird species use high elevations, and that all primary high elevation habitats are important for full life-cycle conservation of this avifauna. Our findings highlight the importance of high elevation habitats to migrating birds from wide-ranging breeding distributions for at least three months of the year, a period equivalent to the length of the breeding season for most species. These results emphasize the need for effective conservation of fragile alpine and other high elevation habitats that are increasingly threatened by local, regional, and global anthropogenic disturbance.
DOI: 10.14288/1.0398103
title: Data from: Small montane cloud forest fragments are important for conserving tree diversity in the Ecuadorian Andes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Montane tropical cloud forests, with their complex topography, biodiversity, high numbers of endemic species, and rapid rates of clearing are a top global conservation priority. However, species distributions at local and landscape scales in cloud forests are still poorly understood, in part because few regions have been surveyed. Empirical work has focused on species distributions along elevation gradients, but spatial variation among forests at the same elevation is less commonly investigated. In this study, the first to compare tree communities across multiple Andean cloud forests at similar elevations, we surveyed trees in five ridge-top forest reserves at the upper end of the ‘mid-elevation diversity bulge’ (1900-2250 masl) in the Intag Valley, a heavily deforested region in the Ecuadorian Andes. We found that tree communities were distinct in reserves located as close as 10 to 35 km apart, and that spatially closer forests were not more similar to one another. Although larger (1500 to 6880 ha), more intact forests contained significantly more tree species (108-120 species/0.1ha) than smaller (30 to 780ha) ones (56-87 species/0.1ha), each reserve had unique combinations of more common species, and contained high proportions of species not found in the others. Results thus suggest that protecting multiple cloud forest patches within this narrow elevational band is essential to conserve landscape-level tree diversity, and that even small forest reserves contribute significantly to biodiversity conservation. These findings can be applied to create management plans to conserve and restore cloud forests in the Andes and tropical montane cloud forests elsewhere.
DOI: 10.14288/1.0398104
title: Data from: The role of pleiotropy in the maintenance of sex in yeast

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;In facultatively sexual species, lineages that reproduce asexually for a period of time can accumulate mutations that reduce their ability to undergo sexual reproduction when sex is favorable. We propagated Saccharomyces cerevisiae asexually for ~800 generations, after which we measured the change in sexual ﬁtness, measured as the proportion of asci observed in sporulation medium. The sporulation rate in cultures propagated asexually at small population size declined by 8%, on average, over this time period, indicating that the majority of mutations that affect sporulation rate are deleterious. Interestingly, the sporulation rate in cultures propagated asexually at large population size improved by 11%, on average, indicating that selection on asexual function effectively eliminated most of the mutations deleterious to sporulation ability. These results suggest that pleiotropy between mutations’ effects on asexual ﬁtness and sexual ﬁtness was predominantly positive, at least for the mutations accumulated in this experimental evolution study. A positive correlation between growth rate and sporulation rate among lines also pro- vided evidence for positive pleiotropy. These results demonstrate that, at least under certain circum- stances, selection acting on asexual ﬁtness can help to maintain sexual function.
DOI: 10.14288/1.0398106
title: Data from: Root effect haemoglobins in fish may greatly enhance general oxygen delivery relative to other vertebrates

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The teleost fishes represent over half of all extant vertebrates; they occupy nearly every body of water and in doing so, occupy a diverse array of environmental conditions. We propose that their success is related to a unique oxygen (O2) transport system involving their extremely pH-sensitive haemoglobin (Hb). A reduction in pH reduces both Hb-O2 affinity (Bohr effect) and carrying capacity (Root effect). This, combined with a large arterial-venous pH change (ΔpHa-v) relative to other vertebrates, may greatly enhance tissue oxygen delivery in teleosts (e.g., rainbow trout) during stress, beyond that in mammals (e.g., human). We generated oxygen equilibrium curves (OECs) at five different CO2 tensions for rainbow trout and determined that, when Hb-O2 saturation is 50% or greater, the change in oxygen partial pressure (ΔPO2) associated with ΔpHa-v can exceed that of the mammalian Bohr effect by at least 3-fold, but as much as 21-fold. Using known ΔpHa-v and assuming a constant arterial-venous PO2 difference (Pa-vO2), Root effect Hbs can enhance O2 release to the tissues by 73.5% in trout; whereas, the Bohr effect alone is responsible for enhancing O2 release by only 1.3% in humans. Disequilibrium states are likely operational in teleosts in vivo, and therefore the ΔpHa-v, and thus enhancement of O2 delivery, could be even larger. Modeling with known Pa-vO2 in fish during exercise and hypoxia indicates that O2 release from the Hb and therefore potentially tissue O2 delivery may double during exercise and triple during some levels of hypoxia. These characteristics may be central to performance of athletic fish species such as salmonids, but may indicate that general tissue oxygen delivery may have been the incipient function of Root effect Hbs in fish, a trait strongly associated with the adaptive radiation of teleosts.
DOI: 10.14288/1.0398107
title: Data from: Individual performance in relation to cytonuclear discordance in a northern contact zone between long-toed salamander (Ambystoma macrodactylum) lineages

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Cytonuclear discordance in contact zones between related lineages is common, with mitochondrial clines often being displaced from clines in nuclear allele frequency. Proposed explanations for such a pattern include adaptive introgression of mtDNA or a neutral wake of mtDNA being left behind following hybrid zone movement. However, studies investigating these hypotheses are rare. Our previous survey of genetic variation in the long-toed salamander (Ambystoma macrodactylum) highlighted a potential case of cytonuclear discordance between two lineages in western Canada. Here, we use additional markers and samples to clarify the extent of this discordance. We simultaneously assess the feeding performance of individuals in a common environment to test for an association between mitotype and individual performance. The genetic results confirm a general pattern of cytonuclear discordance in the focal region. However, we also observed more limited introgression of a diagnostic nuclear marker. Intriguingly, although there were differences in individual performance associated with the transition between mitotypes, these differences were not fully explained by mitotype. Instead, the lowest performance was observed in individuals demonstrating the greatest mismatch between mtDNA and all nuclear markers, suggesting the potential for cytonuclear incompatibilities to be acting. These results highlight the complexity of understanding the causes and consequences of mtDNA introgression and cytonuclear discordance in contact zones.
DOI: 10.14288/1.0398109
title: Data from: Plant–insect interactions: double-dating associated insect and plant lineages reveals asynchronous radiations

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;An increasing number of plant-insect studies using phylogenetic analysis suggest that cospeciation events are rare in plant–insect systems. Instead, nonrandom patterns of phylogenetic congruence are produced by phylogenetically conserved host switching (to related plants) or tracking of particular resources or traits (e.g., chemical). The dominance of host switching in many phytophagous insect groups may make the detection of genuine cospeciation events difficult. One important test of putative cospeciation events is to verify whether reciprocal speciation is temporally plausible. We explored techniques for double-dating of both plant and insect phylogenies. We use dated molecular phylogenies of a psyllid (Hemiptera)–Genisteae (Fabaceae) system, a predominantly monophagous insect–plant association widespread on the Atlantic Macaronesian islands. Phylogenetic reconciliation analysis suggests high levels of parallel cladogenesis between legumes and psyllids. However, dating using molecular clocks calibrated on known geological ages of the Macaronesian islands revealed that the legume and psyllid radiations were not contemporaneous but sequential. Whereas the main plant radiation occurred some 8 million years ago, the insect radiation occurred about 3 million years ago. We estimated that &gt;60% of the psyllid speciation has resulted from host switching between related hosts. The only evidence for true cospeciation is in the much more recent and localized radiation of genistoid legumes in the Canary Islands, where the psyllid and legume radiations have been partially contemporaneous. The identification of specific cospeciation events over this time period, however, is hindered by the phylogenetic uncertainty in both legume and psyllid phylogenies due to the apparent rapidity of the species radiations.
DOI: 10.14288/1.0398110
title: Data from: Rapid increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae) outbreak in pine forests

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae) in lodgepole pine (Pinus contorta) forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on immediate responses of forest understory plant communities is limited. The objective of this study was to examine the effects of D. ponderosae-induced tree mortality on initial changes in diversity and productivity of understory plant communities. We established a total of 110 1-m2 plots across eleven mature lodgepole pine forests to measure changes in understory diversity and productivity as a function of tree mortality and below ground resource availability across multiple years. Overall, understory community diversity and productivity increased across the gradient of increased tree mortality. Richness of herbaceous perennials increased with tree mortality as well as soil moisture and nutrient levels. In contrast, the diversity of woody perennials did not change across the gradient of tree mortality. Understory vegetation, namely herbaceous perennials, showed an immediate response to improved growing conditions caused by increases in tree mortality. How this increased pulse in understory richness and productivity affects future forest trajectories in a novel system is unknown.
DOI: 10.14288/1.0398111
title: Data from: Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via a comparative genome scan of Neochlamisus bebbianae leaf beetles

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;This study uses a comparative genome scan to evaluate the contributions of host plant related divergent selection to genetic differentiation and ecological speciation in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. For each of 15 pairwise population comparisons, we identified "outlier loci" whose strong differentiation putatively reflects divergent selection. Of 447 AFLP loci, 15% were outliers across multiple population comparisons, and low linkage disequilibrium indicated that these outliers derived from multiple regions of the genome. Outliers were further classified as "host-specific" if repeatedly observed in "different-host" population comparisons but never in "same-host" comparisons. Outliers exhibiting the opposite pattern were analogously classified as "host-independent." Host-specific outliers represented 5% of all loci and were more frequent than host-independent outliers, thus revealing a large role for host-adaptation in population genomic differentiation. Evidence that host-related selection can promote divergence despite gene flow was provided by population trees. These were structured by host-association when datasets included host-specific outliers, but not when based on neutral loci, which united sympatric populations. Lastly, three host-specific outliers were highly differentiated in all nine different-host comparisons. Because host-adaptation promotes reproductive isolation in these beetles, these loci provide promising candidate gene regions for future molecular studies of ecological speciation.
DOI: 10.14288/1.0397943
title: Data from: Cooperation can promote rescue or lead to evolutionary suicide during environmental change

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The adaptation of populations to changing conditions may be affected by interactions between individuals. For example, when cooperative interactions increase fecundity, they may allow populations to maintain high densities and thus keep track of moving environmental optima. Simultaneously, changes in population density alter the marginal benefits of cooperative investments, creating a feedback loop between population dynamics and the evolution of cooperation. Here we model how the evolution of cooperation interacts with adaptation to changing environments. We hypothesize that environmental change lowers population size and thus promotes the evolution of cooperation, and that this, in turn, helps the population keep up with the moving optimum. However, we find that the evolution of cooperation can have qualitatively different effects, depending on which fitness component is reduced by the costs of cooperation. If the costs decrease fecundity, cooperation indeed speeds adaptation by increasing population density; if, in contrast, the costs decrease viability, cooperation may instead slow adaptation by lowering the effective population size, leading to evolutionary suicide. Thus, cooperation can either promote or—counter-intuitively—hinder adaptation to a changing environment. Finally, we show that our model can also be generalized to other social interactions by discussing the evolution of competition during environmental change.&lt;/p&gt;
DOI: 10.14288/1.0392643
title: MalawiVitals Android App for Study Data Collection (app)~Improving the early diagnosis of neonatal sepsis in Malawi

description: This is the data collection Android app for the Improving the Early Diagnosis of Neonatal Sepsis in Malawi study. The app is used to collect vital signs data from neonates at multiple time points. Survey field values can be entered via onscreen keypad and respiratory rate (via tapping while watching breaths) and pulse oximetry (via a connected pulse oximeter) are integrated into the app.
DOI: 10.57967/hf/5583
title: Betamina-VRM100shots
DOI: 10.3535/fv3-l65-nyt
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25574/23578
title: Chandra X-ray Observatory ObsId 23578

description: Identification of the Host Galaxy of Swift Short GRBs by the Chandra Sub-arcsecond Position
DOI: 10.3535/4xv-0ef-xsd
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/eby-fq8-0rk
title: Dendrophyllia de Blainville, 1830

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8yr-z1k-m8h
title: †Nucleolites Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k6p-f6r-8xl
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e9n-dav-6yt
title: Crinoidea Miller, 1821

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/wav-w13-cql
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25574/23582
title: Chandra X-ray Observatory ObsId 23582

description: Understanding the X-ray emission from Type IIn supernovae
DOI: 10.3535/rvm-2gm-c4v
title: Atlantoxerus Forsyth Major, 1893

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1r3-rdc-rxn
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zxw-796-9hc
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4pr-lml-3lc
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ta7-1vb-k8h
title: Belemnites

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25574/23599
title: Chandra X-ray Observatory ObsId 23599

description: X-ray Binaries 1 Gyr After a Collision: A Chandra Study of M96 (NGC 3368)
DOI: 10.3535/7jx-6ym-kjk
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l3k-0qr-q4s
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8cn-yeb-57q
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gpw-v1p-82s
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pcx-ddt-q8t
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25574/23600
title: Chandra X-ray Observatory ObsId 23600

description: Luminous binaries at z&gt;8: Chandra detections in Primordial Galaxy Analogs
DOI: 10.3535/8e0-60v-gpf
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e95-6tk-qee
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/y4p-3tv-sc9
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/z08-197-57d
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/87x-ldr-g6x
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c12-x8x-nrj
title: Cardium Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25574/23684
title: Chandra X-ray Observatory ObsId 23684

description: Origin of Unresolved X-ray Emission of Radio-Loud Quasars
DOI: 10.3535/03f-sv7-qcv
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.