Biology subjects

Rueda, M.

Publications and source records attributed to Rueda, M..

6 recordsLinked to original sources

bioRxiv2026

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts

MotivationVariant calling for next-generation sequencing (NGS) data relies on a diverse ecosystem of tools and workflows. Large-scale collaborative studies increasingly adopt federated analysis, where each institution processes sensitive data locally using standardized pipelines. Deploying identical pipelines across multiple centers remains challenging because heterogeneous software environments and computing policies can cause workflow divergence and inconsistent results. ResultsWe developed CBIcall, a workflow-agnostic, configuration-driven framework that runs standardized variant-calling pipelines from raw FASTQ files to analysis-ready VCFs using a single YAML file. An execution driver validates user parameters, enforces compatibility across pipelines, analysis modes, work-flow backends, genome builds, and tool versions, and records structured provenance for each run, ensuring consistent and reproducible pipeline execution across computing environments. CBIcall dispatches validated workflows through Bash or Snakemake backends and provides production-ready pipelines for germline WES, WGS (single-sample or cohort joint genotyping following GATK Best Practices), and mitochondrial DNA analysis. We validated CBIcall on public datasets and deployed it in the EU HEREDITARY project, processing 1,111 samples with both WES and mtDNA pipelines on an institutional HPC system, demonstrating its suitability for reproducible cohort-scale genomic analyses. Availability and implementationCBIcall is open source (GPLv3) and distributed with ready-to-run pipelines; full dependency and installation documentation is available at https://github.com/CNAG-Biomedical-Informatics/cbicall.

bioinformatics↗

bioRxiv2024

TOP-DOWN CLIMATIC PROCESSES MODULATE BIODIVERSITY-FUNCTIONING RELATIONSHIPS ACROSS NORTH AMERICAN FORESTS

Experimental evidence indicates that more diverse communities sustain higher levels of ecosystem functioning. Generally, bottom-up processes accounting for community selection and complementarity effects on biodiversity are used to explain biodiversity effects on ecosystem functioning. However, top-down macroecological processes can also influence the distribution of ecosystem functions across large environmental gradients and, importantly, biodiversity patterns. Here, we tested whether past climate instability, current climate, and climate-driven species abundance explain tree richness gradients, and therefore, determine the relationship between species richness and ecosystem functioning using 137,808 forest inventory plots across continental extents including forests of Canada, the US, and Mexico. Consistent with previous research, we found a positive monotonic relationship between species richness and biomass (measured as level stand basal area) across North American forests. However, structural equation models revealed that the indirect effect of past climate instability, current climate conditions, and climate-driven individuals abundance underlie species richness patterns and the positive covariation between species richness and biomass. The importance of top-down climatic processes varied from boreal to tropical regions, yet their significant effects were pervasive across all forest types, indicating that climate strongly modulates the strength of the relationships between species richness and basal area. Our results help to understand the assembly processes driving the ubiquitous positive monotonic relationship between species richness and basal area across continental extents. This knowledge, obtained from adopting a macroecological perspective, helps understanding biodiversity-functioning relationships, which are usually explained by mechanisms at the community level. Significance statementMore biodiverse communities sustain higher levels of ecosystem functions (BEF hypothesis). The role of biotic interactions among trees within ecological communities determining BEF has been widely studied, but it is not well known how past climatic variability, current climate, and species abundance determine BEF. Using 137,808 forest inventory plots across North American forests located in Canada, the US, and Mexico, we document a positive relationship between tree species richness and stand basal area. Detailed analysis revealed that the positive BEF relationship is underlined by a strong and indirect effect of past and current climate. Our results highlight the importance of top-down climate processes operating at macroecological scales to understand biodiversity-functioning relationships.

ecology↗

bioRxiv2022

Functional traits trade-offs define plant population stability worldwide

O_LIEcological theory posits that temporal stability patterns in plant populations are associated with differences in species ecological strategies. However, empirical evidence is lacking about which traits, or trade-offs, underlie species stability, specially across different ecosystems. C_LIO_LITo address this, we compiled a global collection of long-term permanent vegetation records (>7000 plots from 78 datasets) from a wide range of habitats and combined this with existing trait databases. We tested whether the observed inter-annual variability in species abundance (coefficient of variation) was related to multiple individual traits and multivariate axes of trait variations (PCoA axes). C_LIO_LIWe found that species with greater leaf dry matter content and seed mass were consistently more stable over time (lower variability in species abundance) although other leaf traits played a significant role as well, albeit weaker. Using multivariate axes did not improve predictions by specific traits. C_LIO_LIOur results confirm existing theory, providing compelling empirical evidence on the importance of specific traits, which point at ecological trade-offs in different resource use and dispersal strategies, on the stability of plant populations worldwide. C_LI

ecology↗

bioRxiv2021

LOTVS: a global collection of permanent vegetation plots

Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of vascular plants in permanent plots. With 79 datasets from five continents and 7789 vegetation time-series monitored for at least six years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally fine-grained vegetation time-series derived from permanent plots and made accessible to the research community. As such, it has an outstanding potential to support innovative research in the fields of vegetation science, plant ecology and temporal ecology.

ecology↗

bioRxiv2019

Global mammalian zooregions reveal a signal of past human impacts

Ecologists have long documented that the worlds biota is spatially organized in regions with boundaries shaped by processes acting on geological and evolutionary timescales. Although growing evidence suggests that human impact has been key in how biodiversity is currently assembled, its role as a driver of the geographical organization of biodiversity remains unclear. Here, we quantify the relative importance of human land use from [~]5000 years ago to predict the current assemblage of terrestrial mammals in biogeographical regions across the Earth. Results show that past anthropogenic land use has left an imprint on the taxonomic differentiation of some of the largest biogeographical realms, whereas land use at present stands out as a driver of the taxonomic differences between medium-sized subregions, i.e., within and among continents. Our findings highlight the far-reaching effect that past anthropogenic actions have had on the organization of biodiversity globally.

ecology↗

bioRxiv2018

Human activity is altering the world’s zoogeographical regions

Human activity leading to both species introductions and extinctions is widely known to influence diversity patterns on local and regional scales. Yet, it is largely unknown whether the intensity of this activity is enough to affect the configuration of biodiversity at broader levels of spatial organization. Zoogeographical regions, or zooregions, are surfaces of the Earth defined by characteristic pools of species, which reflect ecological, historical, and evolutionary processes acting over millions of years. Consequently, it is widely assumed that zooregions are robust and unlikely to change on a human timescale. Here, however, we show that human-mediated introductions and extinctions can indeed reconfigure the currently recognized zooregions of amphibians, mammals, and birds. In particular, introductions homogenize the African and Eurasian zooregions in mammals; reshape boundaries with the reallocation of Oceania to the New World zooregion in amphibians; and divide bird zooregions by increasing biotic heterogeneity. Furthermore, the combined effect of amphibian introductions and extinctions has the potential to divide two zooregions largely representing the Old and the New World. Interestingly, the robustness of zooregions against changes in species composition may largely explain such zoogeographical changes. Altogether, our results demonstrate that human activities can erode the higher-level organization of biodiversity formed over millions of years. Comparable reconfigurations have previously been detectable in Earths history only after glaciations and mass extinction events, highlighting the profound and far-reaching impact of ongoing human activity and the need to protect the uniqueness of biotic assemblages from the effects of future species introductions and extinctions.

ecology↗