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opencc-by-4.0Nov 2022View details →

Atmospheric river contributions to ice sheet hydroclimate at the Last Glacial Maximum

This dataset contains the atmospheric river catalogues and the associated precipitation and temperature data for the Preindustrial and Last Glacial Maximum CESM2 simulations presented in the GRL manuscript:  Atmospheric river contributions to ice sheet hydro climate at the Last Glacial Maximum. The atmospheric river catalogue files (zipped) are in netcdf format and organized by year. There are 100 years of data for both simulations.  The Preindustrial simulation catalogue begins in model year 41 and ends in model year 140.  The LGM simulation catalogue begins in model year 1 and ends in year 100. Each yearly file has a temporal resolution of 6 hours (1460 time steps each file) and a spatial resolution of 0.9° x 1.25° (the native resolution of the CESM simulation). A variable in the file called "ar_binary_tag" indicates whether an atmospheric river is present at each grid cell and each tilmestep: 1 indicates an atmospheric river is present; 0 indicates an atmospheric river is not present.  The precipitation and temperature files are 100-year annual or 100-year seasonal averages of atmospheric river precipitation/temperature. See the Methods section of the article for more details on the atmospheric river detection algorithm and precipitation/temperature calculations. Associated article abstract: Atmospheric rivers (ARs) are an important driver of surface mass balance over today’s Greenland and Antarctic ice sheets. Using paleoclimate simulations with the Community Earth System Model, we find ARs also had a key influence on the extensive ice sheets of the Last Glacial Maximum (LGM). ARs provide up to 53% of total precipitation along the margins of the eastern Laurentide ice sheet and up to 22-27% of precipitation along the margins of the Patagonian, western Cordilleran, and western Fennoscandian ice sheets. Despite overall cold conditions at the LGM, surface temperatures during AR events are often above freezing, resulting in more rain than snow along ice sheet margins and conditions that promote surface melt. The results suggest  ARs may have had an important role in ice sheet growth and melt during previous glacial periods and may have accelerated ice sheet retreat following the LGM.

opencc-by-4.0Nov 2022View details →

Data for How to estimate whether preferential trade agreements contribute to international environmental impact shifting. A new methodology and empirical illustration for Switzerland

Raw and processed data for the paper "How to estimate whether preferential trade agreements contribute to international environmental impact shifting. A new methodology and empirical illustration for Switzerland" The raw trade data file is named TradeDataAggregated.rds The raw greenhouse gas footprint data is contained in Output_all.xlsx

opencc-zeroNov 2022View details →

Eco-evolutionary contributions to community trait change in floating aquatic plants

An entire community of organisms may become modified when its environment changes. These modifications can happen through physiological process (plasticity), evolutionary processes (adaptation) or shifts in species composition (sorting). The outcome of these three sources of change constitutes the community's phenotypic response, but how they combine to drive community trait dynamics is not currently well understood. We have conducted a community selection experiment in which communities of short-lived floating aquatic plants were grown in a range of stressful conditions, and measured changes in their body size. Determinants of phenotypic change were assessed with a full community reciprocal transplant which led to estimates of the contributions of plasticity, adaptation, and sorting. Species were modified during the experiment by both plasticity and adaptation, but in either case the magnitude and direction of change differed among species. Sorting and adaptation were of equal magnitude, but tended to act in opposite directions: in conditions where species with large fronds prevailed, each species evolved smaller fronds, and vice versa. We conclude that community trait dynamics cannot be understood simply by extrapolating the adaptive response of any single species to the whole community.

opencc-zeroDec 2022View details →

Data from: Wallace 2: A shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions

These are the occurrence locality datasets used in the example provided in "wallace 2: a shiny app for modeling species niches and distributions redesigned to facilitate expansion via module contributions" published in Ecography (DOI: 10.1111/ecog.06547). The analysis workflow is displayed in the Supporting information of the paper (Fig. S1), and these data are also used in the wallace 2 vignette (<a href="https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html">https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html</a>).

opencc-zeroDec 2022View details →

Data for: Reproductive isolating mechanisms contributing to asymmetric hybridization in Killifishes (Fundulus spp.)

When species hybridize, one F1 hybrid cross type often predominates. Such asymmetry can arise from differences in a variety of reproductive barriers, but the relative roles and concordance of pre-mating, post-mating prezygotic barriers, and post-zygotic barriers in producing these biases in natural animal populations have not been widely investigated. Here, we study a population of predominantly F1 hybrids between two killifish species (Fundulus heteroclitus and Fundulus diaphanus) in which >95% of F1 hybrids have F. diaphanus mothers and F. heteroclitus fathers (D♀×H♂). To determine why F. heteroclitus x F. diaphanus F1 hybrids (H♀×D♂) are so rare, we tested for asymmetry in pre-mating reproductive barriers (female preference, male aggression) at a common salinity (10 ppt) and post-mating, pre-zygotic (fertilization success) and post-zygotic (embryonic development time and hatching success) reproductive barriers at a range of ecologically relevant salinities (0, 5, 10, and 15 ppt). We found that F. heteroclitus females preferred conspecific males, while F. diaphanus females did not, matching the observed cross bias in the wild. Naturally rare H♀×D♂ crosses also had lower fertilization success than all other cross types, and a lower hatching success than the prevalent D♀×H♂ crosses at the salinity found in the hybrid zone centre (10 ppt). Furthermore, the naturally predominant D♀×H♂ crosses had a higher hatching success than F. diaphanus crosses at 10ppt, which may affect their relative abundance. The present study suggests that a combination of incomplete mating, post-mating pre-zygotic and post-zygotic reproductive isolating mechanisms act in concert to produce hybrid asymmetry in this system.

Figs 3-4 in Contribution to the knowledge of the Ichneumoninae (Hymenoptera, Ichneumonidae) of Yemen

Figs 3-4: Habitus of Epomiator yemeniticus nov.sp. ♀ (3) from lateral, (4) from dorsal.

Abb. 2 in Contribution to the preparation and determination of families Anobiidae und Ptinidae (Coleoptera, Teredilia)

Abb. 2: Präpariernadeln mit Fähnchen; lange Präpariernadel für Tropfenentnahme.

Fig. 3-4 in Contribution to the preparation and determination of families Anobiidae und Ptinidae (Coleoptera, Teredilia)

Fig. 3-4: Acid cap bottle; finished preparation.

Fig. 2 in Contribution to the preparation and determination of families Anobiidae und Ptinidae (Coleoptera, Teredilia)

Fig. 2: Dissecting needles with flags; long dissecting needle for taking drops.

Abb. 3-4 in Contribution to the preparation and determination of families Anobiidae und Ptinidae (Coleoptera, Teredilia)

Abb. 3-4: Säurekappenflasche; fertiges Präparat.

opencc-zeroJan 2023View details →

Soil biota diversity and plant diversity both contributed to ecosystem stability in grasslands

Understanding the effects of diversity on ecosystem stability in the context of global change has become an important goal of recent ecological research. However, the effects of diversity at multiple scales and trophic levels on ecosystem stability across environmental gradients remain unclear. Here, we conducted a field survey of α-, β-, and γ-diversity of plants and soil biota (bacteria, fungi, and nematodes) and estimated the temporal ecosystem stability of NDVI in 132 plots on the Mongolian Plateau. After climate and soil environmental variables were controlled for, both the α- and β-diversity of plants and soil biota (mainly via nematodes) together with precipitation explained most variation in ecosystem stability. These findings evidence that the diversity of both soil biota and plants contributes to ecosystem stability. Model predictions of the future effects of global changes on terrestrial ecosystem stability will require field observations of diversity of both plants and soil biota.

opencc-by-4.0Dec 2022View details →

Data for: Recreational land use contributes to the loss of marine biodiversity

This repository includes data for the article: Virtanen, E. A., N. Kallio, M. Nurmi, S. Jernberg, L. Saikkonen, L. Forsblom. Recreational land use contributes to the loss of marine biodiversity, People and Nature.

opencc-by-4.0Jan 2023View details →

Contribution function for the GOLD disk temperature observations

Contribution function for the GOLD disk temperature observations. These are valid for low-solar activity condition. The contents of netCDF files are as follows: dimensions:     n_alts = 91 ;     n_szas = 6 ; variables:     float sol_zen(n_szas) ;         sol_zen:units = "degree" ;         sol_zen:long_name = "Solar Zenith Angle" ;     float altitude(n_alts) ;         altitude:units = "km" ;         altitude:long_name = "Geometric altitude" ;     float CF(n_szas, n_alts) ;         CF:units = "unitless" ;         CF:long_name = "Normalized Contribution Function" ; // global attributes:         :description = "Contribution Function for the GOLD Tdisk at low solar activity condition; Courtesy: J. S. Evans, CPI" ;         :history = "Created 2023-01-26 17:23:54.900047" ;

opencc-zeroFeb 2023View details →

Using inbreeding to test the contribution of non-additive genetic effects to additive genetic variance: A case study in Drosophila serrata

Additive genetic variance, VA, is the key parameter for predicting adaptive and neutral phenotypic evolution. Changes in demography (e.g., increased close-relative inbreeding) can alter VA, but how depends on the, typically unknown, gene action and allele frequencies across many loci. For example, VA increases proportionally with the inbreeding coefficient when allelic effects are additive, but larger (or smaller) increases can occur when allele frequencies are unequal at causal loci with dominance effects. Here, we describe an experimental approach to assess the potential for rare, recessive alleles to inflate VA under inbreeding. Applying a powerful paired pedigree design in Drosophila serrata, we measured 11 wing traits on half-sibling families bred via either random or sibling mating, differing only in homozygosity (not allele frequency). Despite close inbreeding and substantial power to detect small VA, we detected no deviation from the expected additive effect of inbreeding on genetic (co)variances. Our results suggest the average dominance coefficient is very small relative to the additive effect, or that allele frequencies are relatively equal at loci affecting wing traits. We outline the further opportunities for this paired pedigree approach to reveal the characteristics of VA, providing insight into historical selection and future evolutionary potential.

opencc-zeroMar 2023View details →

Data from: The contribution of mutation to variation in temperature-dependent sprint speed in zebrafish, Danio rerio

The contribution of new mutations to phenotypic variation, and the consequences of this variation for individual fitness, are fundamental concepts for understanding genetic variation and adaptation. Here, we investigated how mutation influenced variation in a complex trait in zebrafish, Danio rerio. Typical of many ecologically relevant traits in ectotherms, swimming speed in fish is temperature-dependent, with evidence of adaptive evolution of thermal performance. We chemically induced novel germline point mutations in males and measured sprint speed in their sons at six temperatures (between 16°C and 34°C). Heterozygous mutational effects on speed were strongly positively correlated among temperatures, resulting in statistical support for only a single axis of mutational variation, reflecting temperature-independent variation in speed (faster-slower mode). These results suggest pleiotropic effects on speed across different temperatures, however, spurious correlations arise via linkage, or heterogeneity in mutation number when mutations have consistent directional effects on each trait. Here, mutation did not change mean speed, indicating no directional bias in mutational effects. The results contribute to emerging evidence that mutations may predominantly have synergistic cross-environment effects, in contrast to conditionally neutral or antagonistic effects which underpin thermal adaptation. We discuss several aspects of experimental design that may affect resolution of mutations with non-synergistic effects.

opencc-zeroMar 2023View details →

Seasonal ecosystem linkages contribute to the maintenance of migratory polymorphism in a salmonid population

The influence of resource subsidies on animal growth, survival, and reproduction is well understood, but their ultimate effects on life history have been less explored. Some wild species have a partially migratory life history, wherein migration is dictated based upon threshold traits regulated in part by the seasonal availability of resources. We conducted a large-scale field manipulation experiment where we provided a terrestrial invertebrate subsidy to red-spotted masu salmon. Individuals in stream reaches that received a subsidy had, on average, a 53% increase in growth rate relative to those in control reaches. This increased growth resulted in a greater proportion of individuals reaching the threshold body size and smolting in the autumn. Consequently, 19–55% of females in subsidized reaches became migratory, whereas 0–14% became migratory in the control reaches. Our findings highlight seasonal ecosystem linkage as a key ecosystem property for maintaining migratory polymorphism in partially migratory animals.

opencc-zeroMar 2023View details →

Compiling forty years of guppy research to investigate the factors contributing to (non)parallel evolution

Examples of parallel evolution have been crucial for our understanding of adaptation via natural selection. However, strong parallelism is not always observed even in seemingly similar environments where natural selection is expected to favour similar phenotypes. Leveraging this variation in parallelism within well-researched study systems can provide insight into the factors that contribute to variation in adaptive responses. Here we analyze the results of 36 studies reporting 446 average trait values in Trinidadian guppies, Poecilia reticulata, from different predation regimes. We examine how the extent of predator-driven phenotypic parallelism is influenced by six factors: sex, trait type, rearing environment, ecological complexity, evolutionary history, and time since colonization. Analyses show that parallel evolution in guppies is highly variable and weak on average, with only 24.7% of the variation among populations being explained by predation regime. Levels of parallelism appeared to be especially weak for colour traits, and parallelism decreased with increasing complexity of evolutionary history (i.e., when estimates of parallelism from populations within a single drainage were compared to estimates of parallelism from populations pooled between two major drainages). Suggestive – but not significant – trends that warrant further research include interactions between the sexes and different trait categories. Quantifying and accounting for these and other sources of variation among evolutionary "replicates" can be leveraged to better understand the extent to which seemingly similar environments drive parallel and nonparallel aspects of phenotypic divergence.

opencc-zeroDec 2022View details →

Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree

Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being the most elusive. Ploeotids make up most of this backbone diversity—yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show they are non-monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships between these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single-cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater-dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon.

opencc-by-4.0Feb 2022View details →

Recurrent, founder and hypomorphic variants contribute to shaping the genetic landscape of Joubert syndrome

Introduction: This database includes the raw data linked with the paper “Recurrent, founder and hypomorphic variants contribute to the genetic landscape of Joubert syndrome”. In this paper we reported eleven recurrent variants in seven distinct JS genes occurring in our large European JS cohort, including a previously unreported variant in KIAA0586 (c.1006C>T). Methods: We evaluated the frequencies of these variants in our cohort of >500 European JS patients and compared them with controls (from three large Italian non-JS cohorts and from the gnomAD database), and with an independent cohort of about 600 JS probands from the United States. Results: All variants were markedly enriched in the European JS cohort compared to all controls. When comparing allele frequencies in the two JS cohorts, the Ashkenazi Jewish founder variant (TMEM216 c.218G>T) was significantly enriched in American JS compared to European JS patients, while the MKS1 c.1476T>G variant was about ten times more frequent among European JS. Frequencies of all remaining variants were comparable in the two cohorts. Genotyping of several microsatellite markers across the gene loci in carriers of seven variants identified four novel founder haplotypes. Of note, MKS1 c.1476T>G was consistently detected in compound heterozygosity with deleterious variants in JS patients, while it was found in homozygosity in an unaffected parent. Functional studies on fibroblasts from this healthy carrier and her affected son showed a similarly reduced percentage of ciliated cells compared to unaffected controls, but much shorter cilia in the patient than in the unaffected homozygous parent, consistent with a hypomorphic effect.