cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397706
title: Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection. Key results: Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data. Conclusions: Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
DOI: 10.14288/1.0397708
title: Data from: Linking the wintering and breeding grounds of warblers along the Pacific Flyway

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Long-distance migration is a behavior that is exhibited by many animal groups. The evolution of novel migration routes can play an important role in range expansions, ecological interactions, and speciation. New migration routes may evolve in response to selection in favor of reducing distance between breeding and wintering areas, or avoiding navigational barriers. Many migratory changes are likely to evolve gradually and are therefore difficult to study. Here, we attempt to connect breeding and wintering populations of myrtle warblers (Setophaga coronata coronata) to better understand the possible evolution of distinct migration routes within this species. Myrtle warblers, unlike most other warblers with breeding ranges primarily in eastern North America, have two disjunct overwintering concentrations—one in the southeastern USA and one along the Pacific Coast—and presumably distinct routes to-and-from these locations. We studied both myrtle and Audubon's warblers (S. c. auduboni) captured during their spring migration along the Pacific Coast, south of the narrow region where these two taxa hybridize. Using stable hydrogen isotopes and biometric data, we show that those myrtle warblers wintering along the southern Pacific Coast of North America are likely to breed at high latitudes in Alaska and the Yukon rather than in Alberta or further east. Our interpretation is that the evolution of this wintering range and migration route along the Pacific Coast may have facilitated the breeding expansion of myrtle warblers into northwestern North America. Moreover, these data suggest that there may be a migratory divide within genetically similar populations of myrtle warblers.
DOI: 10.14288/1.0397710
title: Data from: The diet of an endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci, breeding at the Banc d’Arguin, Mauritania

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;In the period 1998–2010 the endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci breeding in Mauritania has decreased in numbers considerably. The causes for this decline are unknown. This study aimed to investigate the diet of the species. We analysed faecal material collected in the breeding colonies in 8 different years. The results show that Mauritanian Spoonbills almost exclusively eat shrimp (59.7%) and small fish (35.4%), the latter being dominated by Gobiidae (20.8%), Soleidae (4.8%) and Mugilidae (2.8%). Another 10 fish families were represented in small proportions. Shrimp were quantified on the basis of (parts of) mandibles present in the samples. All prey items eaten by the Spoonbills were extremely small. Diet composition of adult birds and chicks appeared to be similar. There was great variation in diet composition of adults between years, but there was no trend in any of the major diet components over the study period. This indicates that the decline of the Spoonbill population is not correlated with changes in food composition. Our diet study has been of a qualitative nature. Considering the dramatic population decline we plea for a more detailed ecological study of the species, including a quantitative approach of food intake and foraging conditions.
DOI: 10.14288/1.0397712
title: Data from: Using experimentation to understand the 10-year snowshoe hare cycle in the boreal forest of North America

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Population cycles have long fascinated ecologists from the time of Charles Elton in the 1920s. The discovery of large population fluctuations in undisturbed ecosystems challenged the idea that pristine nature was in a state of balance. The 10-year cycle of snowshoe hares (Lepus americanus Erxleben) across the boreal forests of Canada and Alaska is a classic cycle, recognized by fur traders for more than 300 years. 2. Since the 1930s ecologists have investigated the mechanisms that might cause these cycles. Proposed causal mechanisms have varied from sunspots to food supplies, parasites, diseases, predation, and social behaviour. Both the birth rate and the death rate change dramatically over the cycle. Social behaviour was eliminated as a possible cause because snowshoe hares are not territorial and do not commit infanticide. 3. Since the 1960s large-scale manipulative experiments have been used to discover the major limiting factors. Food supply and predation quickly became recognized as potential key factors causing the cycle. Experiments adding food and restricting predator access to field populations have been decisive in pinpointing predation as the key mechanism causing these fluctuations. 4. The immediate cause of death of most snowshoe hares is predation by a variety of predators, including the Canada lynx (Lynx canadensis Kerr). The collapse in the reproductive rate is not due to food shortage as was originally thought, but is a result of chronic stress from predator chases. 5. Five major issues remain unresolved. First, what is the nature of the predator-induced memory that results in the prolonged low phase of the cycle? Second, why do hare cycles form a travelling wave, starting in the centre of the boreal forest in Saskatchewan and travelling across western Canada and Alaska? Third, why does the amplitude of the cycle vary greatly from one cycle to the next in the same area? Fourth, do the same mechanisms of population limitation apply to snowshoe hares in eastern North American or in similar ecosystems across Siberia? Finally, what effect will climatic warming have on all the above issues? The answers to these questions remain for future generations of biologists to determine.
DOI: 10.14288/1.0397713
title: Data from: Spartina alterniflora genotypic identity affects plant and consumer responses in an experimental marsh community

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;1. Competition and herbivory are ubiquitous processes known to interactively shape plant performance, distribution and community assembly. Likewise, plant genetic variation and associated trait differences can impact both plant-plant and plant-herbivore interactions individually, yet few studies have explored these interactions simultaneously. 2. Salt marsh communities are an ideal system to study these questions, as they are dominated along the Atlantic and Gulf coasts of the United States by a foundation plant species, Spartina alterniflora, with high levels of genetically-based trait variation. Furthermore, consumer pressure and plant competitors are known to influence both the distribution and production of Spartina. We manipulated Spartina genetic identity, neighbor identity (needlerush, Juncus roemerianus), and consumer presence (snail, Littoraria irrorata) in a one-year field experiment in St. Joseph Bay, FL to test how the strength and direction of neighbor and consumer interactions vary by plant genotype. 3. Consumer effects on Spartina were generally stronger and more variable than those of the plant neighborhood, and these effects were generally consistent across Spartina genotypes. However, genotype-specific variation in morphology, phenology, and palatability significantly influenced both consumer and neighbor responses to Spartina: the consumer Littoraria was more likely to climb palatable Spartina genotypes, and neighboring Juncus had shorter stems in the presence of highly productive Spartina genotypes. 4. Synthesis. Our results add to the growing list of examples highlighting the role of intraspecific variation in species interactions, and suggest that variation in these interactions may promote the maintenance of plant genetic variation and community composition.
DOI: 10.14288/1.0397715
title: Data from: Evolution of movement rate increases the effectiveness of marine reserves for the conservation of pelagic fishes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Current debates about the efficacy of no-take marine reserves (MR) in protecting large pelagic fish such as tuna and sharks have usually not considered the evolutionary dimension of this issue, which emerges because the propensity to swim away from a given place, like any other biological trait, will probably vary in a heritable fashion among individuals. Here, based on spatially-explicit simulations, we investigated whether selection to remain in MRs to avoid higher fishing mortality can lead to the evolution of more philopatric fish. Our simulations, which covered a range of life histories among tuna species (skipjack tuna vs. Atlantic Bluefin tuna) and shark species (great white sharks vs. spiny dogfish) suggested that MRs were most effective at maintaining viable population sizes when movement distances were lowest. Decreased movement rate evolved following the establishment of marine reserves, and this evolution occurred more rapidly with higher fishing pressure. Evolutionary reductions in movement rate led to increases in within-reserve population sizes over the course of the 50 years following MR establishment, although this varied among life-histories, with skipjack responding fastest and great white sharks slowest. Our results suggest the evolution of decreased movement can augment the efficacy of marine reserves, especially for species, such as skipjack tuna, with relatively short generation times. Even when movement rates did not evolve substantially over 50 years (e.g., given long generation times or little heritable variation), marine reserves were an effective tool for the conservation of fish populations when mean movement rates were low or MRs were large.
DOI: 10.14288/1.0397716
title: Data from: Three keys to the radiation of angiosperms into freezing environments

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Early flowering plants are thought to have been woody species restricted to warm habitats1, 2, 3. This lineage has since radiated into almost every climate, with manifold growth forms4. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species’ traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits5 and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile6, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.
DOI: 10.15468/dl.8rxukf
title: Occurrence Download

description: A dataset containing 8681 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "DatasetKey is iNaturalist Research-grade Observations",
 "IucnRedListCategory is one of (CR, EN, VU)"
 ]
}

 The dataset includes 8681 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000459-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0397717
title: Data from: Naked mole rats exhibit metabolic but not ventilatory plasticity following chronic sustained hypoxia

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Naked mole rats are among the most hypoxia-tolerant mammals identified and live in chronic hypoxia throughout their lives. The mechanisms underlying this tolerance, however, are poorly understood. Most vertebrates hyperventilate in acute hypoxia and exhibit an enhanced hyperventilation following acclimatization to chronic sustained hypoxia (CSH). Conversely, naked mole rats do not hyperventilate in acute hypoxia and their response to CSH has not been examined. In this study we explored mechanisms of plasticity in the control of the hypoxic ventilatory response (HVR) and hypoxic metabolic response (HMR) of freely behaving naked mole rats following 8-10 days of chronic sustained normoxia (CSN) or CSH. Specifically, we investigated the role of the major inhibitory neurotransmitter γ-amino butyric acid (GABA) in mediating these responses. Our study yielded three important findings. First, naked mole rats did not exhibit ventilatory plasticity following CSH, which is unique among adult animals studied to date. Second, GABA receptor (GABAR) antagonism altered breathing patterns in CSN and CSH animals and modulated the acute HVR in CSN animals. Third, naked mole rats exhibited GABAR-dependent metabolic plasticity following long-term hypoxia, such that the basal metabolic rate was ~25% higher in normoxic CSH animals than CSN animals, and GABAR antagonists modulated this increase.
DOI: 10.14288/1.0397718
title: Data from: Patterns of colonization and spread in the fungal spruce pathogen Onnia tomentosa

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The basidiomycetous fungus Onnia tomentosa is one of the most widespread root rot pathogens in North America. Although the disease is more severe on spruce and pine trees, this pathogen can infect several coniferous species. In order to study the population structure of O. tomentosa, we harvested 180 basidiocarps in a 45-year-old white spruce plantation in western Quebec in autumn 1997, and extracted DNA directly from individual basidiocarps. Using a combination of spatial coordinates and molecular data based on the analysis of two mitochondrial and three nuclear loci, we measured the average genet size and molecular diversity and assessed the relative contribution of basidiospores and vegetative growth to the stand colonization. Most of the sampled basidiocarps that clustered spatially belonged to the same genet. A total of thirty-seven discrete multilocus genets of an average size of 3.42 m were obtained. The genet size distribution was skewed toward smaller genets (&lt; 3 m) that displayed higher diversity than the larger genets (&gt; 3 m). The nuclear loci were in Hardy-Weinberg equilibrium in the larger genets, but not in the smaller genets, which displayed a deficiency of heterozygotes. This suggests a Wahlund effect, whereby different colonization events resulted in expected heterozygosity higher than observed heterozygosity. Using an estimate of the growth rate of the fungus, only a few of the largest genets were approximately the age of the plantation. These observations are consistent with the colonization by basidiospores subsequent to site preparation and tree planting followed by secondary colonization events and vegetative spread.
DOI: 10.14288/1.0397719
title: Data from: Maternal provisioning is structured by species’ competitive neighborhoods

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Differential maternal provisioning of offspring in response to environmental conditions has been argued as ‘the missing link’ in plant life histories. Although empirical evidence suggests that maternal provisioning responses to abiotic conditions are common, there is little understanding of how differences in maternal provisioning manifest in response to competition. Frequency manipulations are commonly employed in ecological studies to assess the strength of interspecific competition, relative to intraspecific competition, and we used frequency manipulations to test how competition in two soil moisture environments affects maternal provisioning of seed mass. Specifically, for 15 pairs comprised from 25 annual plant species that occur in California, we varied the relative frequencies of conspecific to heterospecific competitors from 90% (intraspecific competition) to 10% (interspecific competition). We found that conspecific frequency affected maternal provisioning (seed mass) in 12 of the 25 species (8 significantly (P&lt;0.05), four marginally significantly (P&lt;0.07)), and that these responses included both increased (5 species) and decreased (6 species) seed mass, as well as one species with opposing directions of response to conspecific frequency that depended on the soil moisture environment. Conspecific frequency also affected per capita fecundity (seed number) for 17 of the 25 species (15 significantly (P&lt;0.05), two marginally significantly (P&lt;0.09)), which generally decreased seed number as conspecific frequency increased. The direction and magnitude of frequency-dependent seed mass depended on the identity of the competitor, even among species whose fecundity was not affected by competitor identity; the latter finding reveals competitive differences among species that would otherwise appear to be competitively equivalent. Our research demonstrates how species responses to different competitive environments manifest through maternal provisioning, and that these responses alter previous estimates of environmentally-determined maternal provisioning and reproductive output; future study is needed to understand their combined effects on population and community dynamics.
DOI: 10.14288/1.0397721
title: Data from: Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.
DOI: 10.14288/1.0397722
title: Data from: Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Identifying the genetic bases for color patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here we use natural admixture in a hybrid zone between Audubon’s and myrtle warblers (Setophaga coronata auduboni / S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple SNPs across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that makeup feathers. A carotenoid-based trait that differs between the taxa—throat color—had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits—colors of the eye line and eye spot—show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.