Biology subjects

Molina-Venegas, R.

Publications and source records attributed to Molina-Venegas, R..

6 recordsLinked to original sources

bioRxiv2025

Safeguarding evolutionary history in a biodiversity hotspot: downscaling the EDGE metric to a regional application

In the face of accelerating biodiversity loss, phylogenetically informed approaches offer critical insights for conservation planning from an evolutionary perspective. The EDGE (Evolutionarily Distinct and Globally Endangered) metric combines phylogenetic singularity with extinction risk to identify taxa that represent unique evolutionary history under threat. In this study, we focus on the global conservation relevance of angiosperms native to a regional biodiversity hotspot, the Iberian Peninsula. Our aim was to identify areas with a high concentration of EDGE species and to evaluate how effectively the current protected area network encompasses them. Our findings reveal that threatened evolutionary history is primarily concentrated in mountainous and coastal regions. While several EDGE zones --areas containing unique and endangered evolutionary lineages-- overlap with existing protected areas, particularly in mountains, others harbouring few but evolutionarily unique and highly threatened taxa remain largely unprotected. This study highlights the value of applying global conservation metrics such as EDGE at regional scales. Our results provide a foundation for integrating evolutionary history into conservation prioritization in the Iberian Peninsula and offer a replicable framework for implementing the EDGE approach in other biodiversity-rich regions. Impact statementIn the Iberian Peninsula, there are 22 EDGE zones that account for over 90% of angiosperm threatened evolutionary history.

plant biology↗

bioRxiv2022

Significant phylogenetic signal is not enough to trust phylogenetic predictions

In a recent study, Cantwell-Jones et al. (2022) proposed a list of 1044 species as promising key sources of B vitamins based primarily on phylogenetic predictions. To identify candidate plants, they fitted lambda models of evolution to edible species with known values in each of six B vitamins (232 to 280 species) and used the estimated parameters to predict B-vitamin profiles of edible plants lacking nutritional data (6460 to 6508 species). The latter species were defined as potential sources of a B vitamin if the predicted vitamin content was [≥]15% towards recommended dietary allowances for active females between 31-50 years per 100 g of fresh edible plant material consumed. Unfortunately, the reliability of the predictions that informed the list of candidate species is questionable due to insufficient phylogenetic signal in the data (Pagels {lambda} between 0.171 and 0.665) and a high incidence of species with missing values (over 95% of all the species analyzed in the study). We found that of the 1044 species proposed as promising B-vitamin sources, 626 to 993 species showed accuracies that were indistinguishable from those obtained under a white noise model of evolution (i.e. random predictions conducted in absence of any phylogenetic structure) in at least one of the vitamins, which proves the weakness of the inference drawn from imputed information in the original study. We hope this commentary serves as a cautionary note for future phylogenetic imputation exercises to carefully assess whether the data meet the requirements for the predictions to be valuable, or at least more accurate than expected by chance.

evolutionary biology↗

bioRxiv2022

randtip, a generalized framework to expand incomplete phylogenies using non-molecular phylogenetic information

O_LIThe increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the worlds biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. C_LIO_LIThis prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. C_LIO_LIHere, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package randtip, a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. C_LIO_LIAlthough randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the blind expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow. C_LIO_LIPhylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses. C_LI

evolutionary biology↗

bioRxiv2019

The results of biodiversity-ecosystem functioning experiments are realistic

A large body of research shows that biodiversity loss can reduce ecosystem functioning, thus providing support for the conservation of biological diversity1-4. Much of the evidence for this relationship is drawn from biodiversity-ecosystem functioning experiments (hereafter: biodiversity experiments), in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured5-9. This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly may often be non-random and influenced by external drivers, such as climate or land-use intensification10-18. Despite these repeated criticisms, there has been no comprehensive, quantitative assessment of how experimental and real-world plant communities really differ, and whether these differences invalidate the experimental results. Here, we compare data from two of the largest and longest-running grassland biodiversity experiments globally (Jena Experiment, Germany; BioDIV, USA) to related real-world grassland plant communities in terms of their taxonomic, functional, and phylogenetic diversity and functional-trait composition. We found that plant communities of biodiversity experiments have greater variance in these compositional features than their real-world counterparts, covering almost all of the variation of the real-world communities (82-96%) while also containing community types that are not currently observed in the real world. We then re-analysed a subset of experimental data that included only ecologically-realistic communities, i.e. those comparable to real-world communities. For ten out of twelve biodiversity-ecosystem functioning relationships, biodiversity effects did not differ significantly between the full dataset of biodiversity experiments and the ecologically-realistic subset of experimental communities. This demonstrates that the results of biodiversity experiments are largely insensitive to the inclusion/exclusion of unrealistic communities. By bridging the gap between experimental and real-world studies, these results demonstrate the validity of inferences from biodiversity experiments, a key step in translating their results into specific recommendations for real-world biodiversity management.

ecology↗

bioRxiv2019

Avoiding potential biases in ses.PD estimations with the Picante software package

O_LIFaiths phylogenetic diversity (PD) is one of the most widespread used indices of phylogenetic structure in the eco-phylogenetic literature. The metric became notably popular with the publication of the function pd as part of the Picante R package, which is nowadays a reference software for phylogenetic analyses.\nC_LIO_LIBecause PD is not statistically independent of species richness, the routine procedure is to standardize the observed PD values for unequal richness across samples. The function ses.pd, which is also implemented in the Picante R package, is the reference function to conduct such standardization.\nC_LIO_LIUnfortunately, I have detected an anomaly in the function that may result in biased estimations of standardized PD values, particularly in communities with low species richness (i.e. less than four species) and unbalanced phylogenies.\nC_LIO_LII conduct a simple simulation exercise to illustrate the issue and propose two alternative and easy to implement solutions to go around the problem.\nC_LI

bioinformatics↗

bioRxiv2017

Pleistocene climate change and the formation of regional species pools

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://doi.org/10.24072/pci.evolbiol.100053). Despite the description of bioregions dates back from the origin of biogeography, the processes originating their associated species pools have been seldom studied. Ancient historical events are thought to play a fundamental role in configuring bioregions, but the effects of more recent events on these regional biotas are largely unknown. We use a network approach to identify regional and sub-regional faunas of European Carabus beetles, and analyse the effects of dispersal barriers, niche similarities and phylogenetic history on their configuration. We identify a transition zone matching the limit of the ice sheets at Last Glacial Maximum. While southern species pools are mostly separated by dispersal barriers, in the north species are mainly sorted by their environmental niches. Strikingly, most phylogenetic structuration of Carabus faunas occurred during the Pleistocene. Our results show how extreme recent historical events -such as Pleistocene climate cooling, rather than just deep-time evolutionary processes, can profoundly modify the composition and structure of geographic species pools.

ecology↗