cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397885
title: Data from: The evolution of sex chromosomes in organisms with separate haploid sexes

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The evolution of dimorphic sex chromosomes is driven largely by the evolution of reduced recombination and the subsequent accumulation of deleterious mutations. While these processes are increasingly well understood in diploid organisms, the evolution of dimorphic sex chromosomes in haploid organisms (U/V) has been virtually unstudied theoretically. We analyze a model to investigate the evolution of linkage between fitness loci and the sex-determining region in U/V species. In a second step, we test how prone non-recombining regions are to degeneration due to accumulation of deleterious mutations. Our modeling predicts that the decay of recombination on the sex chromosomes and the addition of strata via fusions will be just as much a part of the evolution of haploid sex chromosomes as in diploid sex chromosome systems. Reduced recombination is broadly favored, as long as there is some fitness difference between haploid males and females. The degeneration of the sex-determining region due to the accumulation of deleterious mutations is expected to be slower in haploid organisms because of the absence of masking. Nevertheless, balancing selection often drives greater differentiation between the U/V sex chromosomes than in X/Y and Z/W systems. We summarize empirical evidence for haploid sex chromosome evolution and discuss our predictions in light of these findings.
DOI: 10.14288/1.0397886
title: Data from: Evaluation of demographic history and neutral parameterization on the performance of Fst outlier tests

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;FST outlier tests are a potentially powerful way to detect genetic loci under spatially divergent selection. Unfortunately, the extent to which these tests are robust to non-equilibrium demographic histories has been under-studied. We developed a landscape-genetics simulator to test the effects of isolation by distance (IBD) and range expansion on FST outlier methods. We evaluated the two most commonly used methods for the identification of FST outliers (FDIST2 and BayeScan, which assume samples are evolutionarily independent) and two recent methods (FLK and Bayenv2, which estimate and account for evolutionary non-independence). Parameterization with a set of neutral loci (“neutral parameterization”) always improved the performance of FLK and Bayenv2, while neutral parameterization caused FDIST2 to actually perform worse in the cases of IBD or range expansion. BayeScan was improved when the prior odds on neutrality was increased, regardless of the true odds in the data. On their best performance, however, the widely-used methods had high false-positive rates for IBD and range expansion and were outperformed by methods that accounted for evolutionary non-independence. In addition, default settings in FDIST2 and BayeScan resulted in many false positives under balancing selection. However, all methods did very well if a large set of neutral loci is available to create empirical p-values. We conclude that in species that exhibit IBD or have undergone range expansion, many of the published FST outliers based on FDIST2 and BayeScan are probably false positives, but FLK and Bayenv2 show great promise for accurately identifying loci under spatially-divergent selection.
DOI: 10.14288/1.0397887
title: Data from: Fixation probability in a haploid-diploid population

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species.
DOI: 10.14288/1.0397888
title: Data from: Do correlated responses to multiple environmental changes exacerbate or mitigate species loss?

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Biological communities face multiple global changes simultaneously, and predicting how they will respond remains a key challenge. Co-tolerance theory offers a framework for understanding how species-level responses to multiple stressors affect community properties. Co-tolerance theory predicts that positive correlations in species responses (i.e., species that are susceptible to one stressor are more likely to be highly susceptible to a second) lessen total species loss, essentially because species cannot be eliminated from a community twice. However, it is unclear whether several of the tenets of co-tolerance theory describe real-world communities, and what consequences result from such deviations. Here, we use an empirical dataset of bird community response to land-use change over a climate gradient to examine co-tolerance theory’s tenet that environmental changes only harm species (not benefit them). We show that this tenet is not met, and then use simulations to examine how predictions of total species richness and community intactness vary when multiple environmental changes both harm and benefit particular species in the community. Finally, we conduct a sensitivity analysis, examining how the average species response to environmental change, as well as the variance among species, can further alter predictions. Overall, we find that predictions of co-tolerance theory can break down when communities contain species that benefit from some environmental changes. As a result, the presence of multiple environmental changes can either compound or mitigate species loss when species’ responses are positively correlated, preventing a one-size-fits-all statement regarding the effects of correlated responses. This finding highlights the need to carefully consider the underlying mechanisms of community change when making policy assessments regarding the consequences of correlations of species responses to environmental impacts.
DOI: 10.14288/1.0397889
title: Data from: Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes. In this study, we utilized RNA-seq to assess transcriptome-wide gene expression in the muscle of Atlantic killifish (Fundulus heteroclitus) from a population that contains segregating variation in mitochondrial genotype. We examined gene expression plasticity in response to 5°C acclimation and the effects of mitochondrial genotype on this plasticity. Cold acclimation resulted in changes in gene expression consistent with up-regulation of genes involved in many cellular functions, including spliceosomal and proteasomal processes, and with down-regulation of genes involved in extracellular matrix, muscle contraction and oxidative phosphorylation functions. There were few differences in gene expression between killifish with different mitochondrial genotypes: 14 genes demonstrated significant interactions between mitochondrial genotype and acclimation temperature and 3 genes demonstrated effects of mitochondrial genotype alone. These results indicate that variation in mitochondrial genotype has modest effects on gene expression; the majority of which are revealed as differences in plasticity as a result of environmental change.
DOI: 10.14288/1.0397890
title: Data from: Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Adaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL Sign Test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs, support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes, and demonstrates that some trait transitions between species could have involved few, large effect genetic changes, allowing rapid responses to new environmental conditions.
DOI: 10.14288/1.0397891
title: Data from: Robustness to noise in gene expression evolves despite epistatic constraints in a model of gene networks

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Stochastic noise in gene expression causes variation in the development of phenotypes, making such noise a potential target of stabilizing selection. Here we develop a new simulation model of gene networks to study the adaptive landscape underlying the evolution of robustness to noise. We find that epistatic interactions between the determinants of the expression of a gene and its downstream effect impose significant constraints on evolution, but these interactions do allow the gradual evolution of increased robustness. Despite strong sign epistasis, adaptation rarely proceeds via deleterious intermediate steps, but instead occurs primarily through small beneficial mutations. A simple mathematical model captures the relevant features of the single-gene fitness landscape and explains counterintuitive patterns, such as a correlation between the mean and standard deviation of phenotypes. In more complex networks, mutations in regulatory regions provide evolutionary pathways to increased robustness. These results chart the constraints and possibilities of adaptation to reduce expression noise and demonstrate the potential of a novel modeling framework for gene networks.
DOI: 10.14288/1.0397900
title: Data from: Conserving evolutionary history does not result in greater diversity over geological timescales

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Alternative prioritization strategies have been proposed to safeguard biodiversity over macro-evolutionary timescales. The first prioritizes the most distantly related species (maximizing phylogenetic diversity) in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over paleontological time scales. We consider the performance of the two schemes across ten dated species-level paleo-phylogenetic trees ranging from foraminifera to dinosaurs. We find that prioritizing phylogenetic diversity for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared to random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing phylogenetic diversity for conservation, long-term species production might not be one of them.
DOI: 10.15468/dl.5fbmrr
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eugenia jambos Blanco, 1837",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Occurrence evidence)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000465-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.14288/1.0397902
title: Data from: Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas-fir forest

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and R. vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas-fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. R. vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared to xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes.
DOI: 10.14288/1.0397903
title: Data from: Lineage-specific mapping of quantitative trait loci

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;We present an approach for quantitative trait locus (QTL) mapping, termed "lineage-specific QTL mapping", for inferring allelic changes of QTL evolution along branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. While comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkeyflower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage- specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed.
DOI: 10.14288/1.0397904
title: Data from: Heterospecific eavesdropping in ant-following birds of the Neotropics is a learned behaviour

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Animals eavesdrop on other species to obtain information about their environments. Heterospecific eavesdropping can yield tangible fitness benefits by providing valuable information about food resources and predator presence. The ability to eavesdrop may therefore be under strong selection, although extensive research on alarm-calling in avian mixed-species flocks has found only limited evidence that close association with another species could select for innate signal recognition. Nevertheless, very little is known about the evolution of eavesdropping behaviour and the mechanism of heterospecific signal recognition, particularly in other ecological contexts, such as foraging. To understand whether heterospecific eavesdropping was an innate or learned behaviour in a foraging context, we studied heterospecific signal recognition in ant-following birds of the Neotropics, which eavesdrop on vocalizations of obligate ant-following species to locate and recruit to swarms of the army ant Eciton burchellii, a profitable food resource. We used a playback experiment to compare recruitment of ant-following birds to vocalizations of two obligate species at a mainland site (where both species are present) and a nearby island site (where one species remains whereas the other went extinct approx. 40 years ago). We found that ant-following birds recruited strongly to playbacks of the obligate species present at both island and mainland sites, but the island birds did not recruit to playbacks of the absent obligate species. Our results strongly suggest that (i) ant-following birds learn to recognize heterospecific vocalizations from ecological experience and (ii) island birds no longer recognize the locally extinct obligate species after eight generations of absence from the island. Although learning appears to be the mechanism of heterospecific signal recognition in ant-following birds, more experimental tests are needed to fully understand the evolution of eavesdropping behaviour.
DOI: 10.14288/1.0397905
title: Data from: Papuaneon, a new genus of jumping spiders from Papua New Guinea (Araneae: Salticidae: Neonini)

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The genus Neon Simon stands alone as a phylogenetically isolated astioid jumping spider, the only member of the Neonini. The new genus Papuaneon is established for the jumping spider Papuaneon tualapa sp. nov. from Papua New Guinea. Resembling a large, hirsute Neon, it is here shown to be the sister group to Neon, based on data from the nuclear 28S and Actin 5C, and the mitochondrial 16SND1 region. Photographs of living specimens are provided.
DOI: 10.14288/1.0397906
title: Data from: The availability of research data declines rapidly with article age

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Policies ensuring that research data are available on public archives are increasingly being implemented at the government, funding agency, and journal level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term, and indeed many studies have found that authors are often unable or unwilling to share their data. However, there are no systematic estimates of how the availability of research data changes with time since publication. We therefore requested datasets from a relatively homogenous set of 516 articles published between 2 and 22 years ago, and found that availability of the data was strongly affected by article age. For papers where the authors gave the status of their data, the odds of a dataset being extant fell by 17% per year. In addition, the odds that we could find a working email address for the first, last or corresponding author fell by 7% per year. Our results reinforce the notion that, in the long term, research data cannot be reliably preserved by individual researchers, and further demonstrate the urgent need for policies mandating data sharing via public archives.
DOI: 10.14288/1.0397908
title: Data from: Estimations of evapotranspiration in an age sequence of Eucalyptus plantations in subtropical China

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;Eucalyptus species are widely planted for reforestation in subtropical China. However, the effects of Eucalyptus plantations on the regional water use remain poorly understood. In an age sequence of 2-, 4- and 6-year-old Eucalyptus plantations, the tree water use and soil evaporation were examined by linking model estimations and field observations. Results showed that annual evapotranspiration of each age sequence Eucalyptus plantations was 876.7, 944.1 and 1000.7 mm, respectively, accounting for 49.81%, 53.64% and 56.86% of the annual rainfall. In addition, annual soil evaporations of 2-, 4- and 6-year-old were 318.6, 336.1, and 248.7 mm of the respective Eucalyptus plantations. Our results demonstrated that Eucalyptus plantations would potentially reduce water availability due to high evapotranspiration in subtropical regions. Sustainable management strategies should be implemented to reduce water consumption in Eucalyptus plantations in the context of future climate change scenarios such as drought and warming.