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opencc-zeroSep 2020View details →

Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"

Trait-based ecology suggests that abiotic filtering is the main mechanism structuring the regional species pool in different subsets of habitat-specific species. At more local spatial scales, other ecological processes may add on giving rise to complex patterns of functional diversity (FD). Understanding how assembly processes operating on the habitat-specific species pools produce the locally observed plant assemblages is an ongoing challenge. Here, we evaluated the importance of different processes to community assembly in an alpine fellfield, assessing its effects on local plant trait FD. Using classical randomization tests and linear mixed models, we compared the observed FD with expectations from three null models that hierarchically incorporate additional assembly constraints: stochastic null models (random assembly), independence null models (each species responding individual and independently to abiotic environment), and co-occurrence null models (species responding to environmental variation and to the presence of other species). We sampled species composition in 115 quadrats across 24 locations in the central Pyrenees (Spain) that differed in soil conditions, solar radiation and elevation. Overall, the classical randomization tests were unable to find differences between the observed and expected functional patterns, suggesting that the strong abiotic filters that sort out the flora of extreme regional environments blur any signal of other local processes. However, our approach based on linear mixed models revealed the signature of different ecological processes. In the case of seed mass and leaf thickness, observed FD significantly deviated from the expectations of the stochastic model, suggesting that fine-scale abiotic filtering and facilitation can be behind these patterns. Our study highlights how the hierarchical incorporation of ecological additional constraints may shed light on the dim signal left by local assembly processes in alpine environments.

opencc-zeroMar 2024View details →

Data and code from: Similar trait-based successional assembly in native and introduced plants despite species pool differences

What drives the composition of invaded communities and the local abundance of introduced species are key questions in ecology. Community-assembly theory provides a useful framework for addressing these questions. Specifically, the environmental filtering model of community assembly predicts that a species' presence and abundance in a community depends on the interaction between its functional traits and the local environmental filters. However, for introduced species, larger-scale dispersal and introduction-related filters may restrict their regional trait pool. Here we tested this framework using long-term data from 50+ years of old-field vegetation succession. We asked whether native and introduced plant assemblages followed the same trait-based assembly rules. We also asked whether local functional dissimilarities between the two can be explained by regional species pool differences, a possibility that has rarely been addressed. We found strong similarities in the assembly processes of native and introduced plants. Average height and seed mass of both groups increased over time, consistent with previous studies of old-field succession. Moreover, the two showed similar trait-abundance relationships. While there were also some differences, particularly in their trait-incidence relationships, these differences appeared to be minor.Further, we identified species pool constraints on introduced species, and found that the exotic species pool was biased towards early successional traits. Lastly, we found that highly invasive exotic species were also likely to deviate from the expected trait-abundance relationship, suggesting a link between the two. These results suggest that introduced species generally follow the same assembly rules as native species. They also indicate that species pool differences can result in local functional composition differences, even when the two groups follow the same assembly rules. Moreover, there may be a link between species invasiveness and deviation from assembly rules, which, if further confirmed, provides a potential method of identifying strong invaders.

openother-openAug 2021View details →

Data and Codes used in Alonso-Crespo et al (2021) Assembly history modulates vertical root distribution in a grassland experiment.

This repository contains the raw data, the RootPainter model and the annotated R and Python codes supporting the results reported in the following paper: Alonso-Crespo et al (2021) Assembly history modulates vertical root distribution in a grassland experiment.

opencc-zeroMay 2024View details →

Code for: Landform and lithospheric development contribute the assembly of mountain floras in China

Although it is well documented that mountains tend to exhibit high biodiversity, how geological processes affect the assemblage of montane floras is a matter of ongoing research. Here, we explore landform-specific differences among montane floras based on a dataset comprising 17,576 angiosperm species representing 140 Chinese mountain floras, which we define as the collection of all angiosperm species growing on a specific mountain. Our results show that igneous bedrock (granitic and karst-granitic landforms) is correlated with higher species richness and phylogenetic overdispersion, while the opposite is true for sedimentary bedrock (karst, Danxia, and desert landforms), which is correlated with phylogenetic clustering. Furthermore, we show that landform type was the primary determinant of the assembly of evolutionarily older species within floras, while climate was a greater determinant for younger species. Our study indicates that landform type not only affects montane species richness, but also contributes to the composition of montane floras. To explain the assembly and differentiation of mountain floras, we propose the 'floristic geo-lithology hypothesis', which highlights the role of bedrock and landform processes in montane floristic assembly and provides insights for future research on speciation, migration, and biodiversity in montane regions.

opencc-by-4.0Jun 2024View details →

Code and data for: Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Evolutionary assembly of the plant terrestrialization toolkit from protein domains <ul> <li>We want to trace the evolutionary predisposition the green lineage had at the time of terrestrialization.</li> <li>Terrestrialization is a complete change in environment from water, and these acted like new and/or intensified stress factors on the green lineage.</li> <li>Thus, in order to trace the evolutionary predisposition which led to successful overcoming of challenges of a new environment, we carefully annotate, dissect and analyse the stress proteome of the extant Green lineage.</li> </ul> Key Concepts <ul> <li>Already existing Concept: <ul> <li>Orthology</li> </ul> </li> <li>New/Redefined Concept <ul> <li>Embryophytic Domain: Protein domain which has an Embryophytic ancestor, that is, present in at least one Bryophyte species and at least one Tracheophyte species</li> <li>Latent Genetic Potential (LGP): Key (functional) Embryophytic protein domains having Last Common Ancestor (LCA) prior to the LCA of protein with corresponding function</li> </ul> </li> </ul> Data: (Figure 1 A) <ul> <li>We take 6 species from Cholorophyte algae lineage, 7 from Streptophyte algae lineage, 5 from Bryophyte lineage and 14 from Tracheophyte lineage. 5 species from Cyanobacteria were taken as an outgroup lineage.</li> </ul> Stress-annotation (Figure 1B) <ul> <li>First 57,796 orthogroups were obtained from 37 proteome. This is computed by using OrthoFinder2.</li> <li>Next we need to annotate stress-related proteins across our dataset. Following are existing ways of annotation: <ul> <li>Extensive experiments have been done on A.thaliana and P.patens in the green lineage. Thus, we stress-annotated 37 proteomes using TAIR10 and PEATmoss respectively. From this method, we stress-annotated 4,902 orthogroups</li> <li>Eggnogmapper is a known tool with an extensive database used for gene ontology purposes. We stress-annotated 17,349 orthogroups.</li> </ul> </li> <li>In order to avoid experimental bias and tool-based randomness we overlap the two methods to have our final stress-annotation. We finally filtered 2,475 stress-annotated orthogroups from 57,796 orthogroups.</li> </ul> Overview of Stress-annotation (Figure 1C, 1D) <ul> <li>To have an overview of stress-annotation, overlaps of stress-annotated protein domains, proteins and orthogroups across our dataset lineages and various response to stresses are shown.</li> </ul> Distribution of Stress-annotation (Figure 2) <ul> <li>Using the overlap annotation approach explained earlier, the stress-annotated orthogroups and corresponding protein domains are in Figure 2A. A standard pattern is observed in both, that is, the unique number of stress orthogroups and protein domains increase from Cyanobacteria to Tracheophytes. The number of proteins and average number of protein domains also increases similarly.</li> <li>Top 10 bursts of protein domains from one lineage to the next is shown in Figure 2B.</li> </ul> Changes in stress-annotation with respect to Protein Domains (Figure 3) <ul> <li>Figure 3 is a 4-dimensional plot with the following parameters: Species(37), Protein Domains (100), Number of Orthgogroups with Protein Domain (size of circle), Number of Proteins with Protein Domain (Color of circle). The plot is sorted from top to bottom based on the number of orthogroups, and the top 100 protein domains are chosen for the plot.</li> <li>This plot is used to express an overview of the most significant occurances of sub- and neo-functionalizations. Here, each orthogroup is considered to be a protein family. 2 protein families can have an overlapping number of functions. That is why there are more than 1 orthogroup which have the same protein domain.</li> </ul> Assembling LGP from protein domains (Figure 4) - refer to Key Concepts to understand LGP <ul> <li>In Figure 1A, we show 2 categories (x/y) of orthogroups at each node (a,b,c,d,e,f). The number y for example at node b indicates the number of orthogroups (4) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP (or key Embryophytic protein domains) in Charophyceae. The number x at node b indicates the number of orthogroups (131) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP in all the rest of the lineages (Charophyceae+Klebsormidiophyceae+Chlorokybophyceae+Mesostigmatophyceae+Chlorophytes) in the figure.</li> <li>Since we are concerned about the LGP for Land Plants (Embryophytes), we look at node a. Next, we functionally annotate 96 orthogroups. 50 annotations that occur the most number of times is shown in Figure 4B.</li> <li>In Figure 4C, we can see in which species the key Embryophytic Domains are present whose proteins and protein families are only seen in Embryophytes.</li> </ul> Thus, from the final figure we can trace the LGP present at the time of terrestrialization in the LCA of Land Plants. Database files: These are intermediate files used in code for different figures. Following is the link to access them:<a href="https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c" rel="nofollow">https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c</a> [OR]<a href="https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA" rel="nofollow">https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA</a>

opencc-by-4.0Sep 2024View details →

Data and code from: Species interactions drive continuous assembly of freshwater communities in stochastic environments

Understanding the factors driving the maintenance of long-term biodiversity in changing environments is essential for improving restoration and sustainability strategies in the face of global environmental change. Biodiversity is shaped by both niche and stochastic processes, however the strength of deterministic processes in unpredictable environmental regimes is highly debated. Since communities continuously change over time and space -- species persist, disappear or (re)appear -- understanding the drivers of species gains and losses from communities should inform us about whether niche or stochastic processes dominate community dynamics. Applying a nonparametric causal discovery approach to a 30-year time series containing annual abundances of benthic invertebrates across 66 locations in New Zealand rivers, we found a strong \hl{negative} causal relationship between species gains and losses directly driven by predation indicating that niche processes dominate community dynamics. Despite the unpredictable nature of these system, environmental noise was only indirectly related to species gains and losses through altering life history trait distribution. Using a stochastic birth-death framework, we demonstrate that the negative relationship between species gains and losses can not emerge without strong niche processes. Our results showed that even in systems that are dominated by unpredictable environmental variability, species interactions drive continuous community assembly.

opencc-by-4.0Nov 2024View details →

Efficiency of thermoremanent magnetization acquisition in vortex-state particle assemblies: Dataset and Codes

When magma cools, crystallized magnetic minerals can record the ambient magnetic field. If these mineral grains are sufficiently small, they may retain that magnetic record for billions of years. This phenomenon enables paleomagnetists to study the direction and intensity of ancient magnetic fields on Earth and other planets. A key task is determining the number of magnetic particles required to reliably record such a field, as well as understanding the influence of grain size and shape on this process. Here, we present a dataset from the study titled "Efficiency of Thermoremanent Magnetization Acquisition in Vortex-State Particle Assemblies," which integrates micromagnetic modeling and probabilistic magnetic state partitioning to address these questions. The dataset includes codes for the micromagnetic simulations and data from all the simulations conducted.

opencc-by-4.0Nov 2024View details →

Code used for the assembly of a wisent genome

copy of the GitHub repository https://github.com/cbortoluzzi/WisentGenomeAssembly

publicMay 2024View details →

Code for: Landform and lithospheric development contribute the assembly of mountain floras in China

Open the record for dataset details and reuse information.

publicMar 2024View details →

Data and code from: Similar trait-based successional assembly in native and introduced plants despite species pool differences

Open the record for dataset details and reuse information.

publicSep 2020View details →

Data and code from "A dimmer shade of pale: revealing the faint signature of local assembly processes on the structure of strongly filtered plant communities"

Open the record for dataset details and reuse information.

openother-openAug 2020View details →

Code and data for Assembly rules of helminth parasite communities in grey mullets: combining components of diversity

Raw data analysed and a step-by-step summary of the R functions and packages used in Llopis-Belenguer, C., Pavoine, S., Blasco-Costa, I., Antonio Balbuena, J., 2020. Assembly rules of helminth parasite communities in grey mullets: combining components of diversity. International Journal for Parasitology. DOI: 10.1016/j.ijpara.2020.06.006

opencc-by-4.0Nov 2023View details →

Input and output data and code for PPS2 on 333 vertebrate and111 plant genome assemblies, and for DDS2+ on fungal genome assemblies

The datasets contain PPS2 and DDS2+ source and binary code, other scripts, and some input and output data. Please see the README file after unpacking it. The absolute paths in the scripts need to be modified in order to duplicate the results in this dataset. Most of the input and output data have to be removed from the datasets for quick uploading and downloading; otherwise, the datasets would exceed the 50-Gb size limit.

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".

Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"

Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".