Biology subjects

Verdu, M.

Publications and source records attributed to Verdu, M..

7 recordsLinked to original sources

bioRxiv2026

Rare plants can make an important contribution to sustain local biodiversity through biological interactions

Plants, as structural elements of habitats, contribute greatly to the maintenance of local biodiversity through their biological interactions. In this study we explore whether their rarity, according to Rabinowitzs (1981) three criteria, is related to the richness and diversity of arthropods and other plants they are associated to, in a gypsum-rich steppe. We first analysed whether the geographic abundance and ecological specialisation of 32 characteristic and dominant plant species are related to the diversity (richness and phylogenetic diversity (MPD)) and degree of local specialisation of arthropods associated with them (1,694 taxa). Then, we focused on a non endemic and non specialized plant in the study area (Krascheninnikovia ceratoides) to explore the effect of population size on two types of interactions: aerial arthropods and plant facilitation. Results indicate that: 1) plant species abundance (geographical range) is not related to the richness or MPD of communities of associated arthropods, 2) plant species ecological specialization (edaphic endemisms or gypsophiles) do not contribute differentially to the maintenance of singular arthropod communities, and 3) the community of aerial arthropods and plants interacting with K. ceratoides in a small population are not necessarily less diverse than those in patches of similar size in a large population. Results also revealed that the two plant species with fewer interactions (one rare, one widespread) do show the highest singularity in their interactions with arthropods. Our study illustrates the important contribution of rare plants to the conservation of local biodiversity.

ecology↗

bioRxiv2024

An accelerating, decreasing phylogenetic trend in SARS-CoV-2 genome compositional heterogeneity during the pandemic

The rapid evolution of SARS-CoV-2 during the pandemic, driven by a plethora of mutations, many of which enable the virus to evade host resistance, has likely altered its genomes compositional structure (i.e. the arrangement of compositional domains of varying lengths and nucleotide frequencies within the genome). To explore this hypothesis, we summarize the evolutionary effects of these mutations by computing the Sequence Compositional Complexity (SCC) in random datasets of fully sequenced genomes. Phylogenetic ridge regression of SCC against time reveals a striking downward evolutionary trend, as well as an increasing rate of change, suggesting the ongoing adaptation of the viruss genome structure to the human host. Other genomic features, such as strand asymmetry, the effective number of K-mers, and the depletion of CpG dinucleotides, each linked to the viruss adaptation to its human host, also exhibit decreasing phylogenetic trends over the course of the pandemic, along with strong phylogenetic correlations to SCC. Overall, our findings suggest an accelerated, genome-wide evolutionary trend toward a more symmetric and homogeneous genome compositional structure in SARS-CoV-2.

evolutionary biology↗

bioRxiv2023

Local-scale divergent selection in a Mediterranean pine

The effects of selection on an organisms genome are hard to detect on small spatial scales, as gene flow can erase signatures of local adaptation. Most genome scans to detect signatures of environmental selection are performed on large spatial scales, however divergent selection on the local scale (e.g. between contrasting soil conditions) has also been demonstrated, in particular for herbaceous plants. Here we hypothesize that in topographically complex landscapes, microenvironment variability is strong enough to leave a selective footprint in genomes of long-lived organisms. To test this, we investigated paired south- versus north-facing Pinus pinaster stands in a Mediterranean mountain area. While north-facing (mesic) stands experience less radiation, south facing (xeric) stands represent especially harsh conditions, particularly during the dry summer season. Outlier detection revealed five putatively adaptive loci out of 4,034, two of which encoded non-synonymous substitutions. Additionally, one locus showed consistent allele frequency differences in all three stand pairs indicating divergent selection despite high gene flow on the local scale. Functional annotation of these candidate genes revealed biological functions related to abiotic stress response in other species. Our study highlights how divergent selection shapes the functional genetic variation within populations of long-lived forest trees on local spatial scales.

plant biology↗

bioRxiv2022

The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS CoV 2 coronavirus

Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus has accumulated an important amount of genetic and genomic variability through mutation and recombination events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize all this sequence variability by computing the Sequence Compositional Complexity (SCC) in more than 23,000 high-quality coronavirus genome sequences from across the globe, covering the period spanning from the start of the pandemic in December 2019 to March 2022. In early samples, we found no statistical support for any trend in SCC values over time, although the virus as a whole appears to evolve faster than Brownian Motion expectation. However, in samples taken after the first Variant of Concern (VoC) with higher transmissibility (Alpha) emerges, and controlling for phylogenetic and sampling effects, we were able to detect a statistically significant trend for decreased SCC values over time. SARS-CoV-2 evolution towards lower values of genome heterogeneity is further intensified by the emergence of successive, widespread VoCs. Concomitantly to the temporal reduction in SCC, its absolute evolutionary rate kept increasing toward the present, meaning that the SCC decrease itself accelerated over time. As compared to Alpha or Delta variants, the currently dominant VoC, Omicron, shows much stronger trends in both SCC values and rates over time. These results indicate that the increases in fitness of variant genomes associated to a higher transmissibility leads to a reduction of their genome sequence heterogeneity, thus explaining the general slowdown of SCC along with the pandemic course.

genomics↗

bioRxiv2022

The interplay between habitat fragmentation and life traits affects specialization in lichen symbioses

O_LIInteractions between organisms are determined by species traits and differ in specialization, from generalist to highly specialized relationships. Although we expect that the effect of habitat loss and fragmentation on the abundance and survival of species depends on their degree of specialization, few studies have deepened into the interplay between interaction specialization and habitat loss. C_LIO_LIHere, we investigate the combined effect of habitat fragmentation and life traits (growth type and reproductive mode) on the specialization of lichen-forming fungi (mycobionts) towards its photosynthetic partners (photobionts) in lichen symbioses. C_LIO_LIWe studied mycobiont specialization in epiphytic lichen communities present in ten fragments of Quercus rotundifolia trees embedded in an agricultural matrix. Both mycobionts and photobionts were identified through DNA sequencing and mycobiont specialization was measured through interaction parameters calculating the relative number of interactions (normalized degree; ND) and the specialization of each species based on its discrimination from a random selection of partners (d). Phylogenetic generalized linear mixed models were used to analyze the effect of patch size as well as the life traits growth type (crustose, foliose, fruticose) and reproduction mode (sexual vs asexual) on mycobiont specialization. C_LIO_LIBoth mycobiont and photobiont richness along the patch size gradient followed a hump-back pattern, which was more pronounced in photobionts. Mycobionts forming crustose biotypes established the largest number of interactions. Mycobiont specialization (d) was larger for fruticose and foliose biotypes and for species with vegetative reproduction. Along the gradient of fragment size, the relative number of interactions decreased and the specialization of mycobionts with vegetative reproduction increased. C_LIO_LISynthesis: The analysis of mycobiont specialization towards their photobionts in communities of epiphytic lichens in a fragmented Mediterranean forest revealed that the interaction between species life traits and habitat loss on specialization cannot be neglected. The results also pointed to the ability of some species to modulate their interactions to certain extent, suggesting that species might have a greater resilience to abiotic changes than expected, presumably creating extinction debt or even avoiding extinction processes to some extent. C_LI ResumenO_LILas interacciones entre organismos estan determinadas por los rasgos funcionales de las especies y difieren en su grado de especializacion, desde interacciones generalistas hasta las altamente especializadas. Aunque se espera que el efecto de la perdida y fragmentacion del habitat sobre la abundancia y la supervivencia de las especies dependa de su grado de especializacion, pocos estudios han profundizado en la interaccion entre la especializacion de las interacciones y la perdida de habitat. C_LIO_LIEn este articulo investigamos el efecto combinado de la fragmentacion del habitat y los rasgos funcionales de las especies (tipo de crecimiento y modo reproductivo) en la especializacion de los hongos liquenizados (micobiontes) hacia sus socios fotosinteticos (fotobiontes) en las simbiosis de liquenes. C_LIO_LISe estudio la especializacion de micobiontes en comunidades de liquenes epifitos presentes en diez fragmentos de arboles de Quercus rotundifolia incrustados en una matriz agricola. Tanto los micobiontes como los fotobiontes fueron identificados mediante la secuenciacion del ADN y la especializacion de los micobiontes se midio a traves de parametros de interaccion calculando el numero relativo de interacciones (grado normalizado; ND) y la especializacion de cada especie en funcion de su discriminacion de una seleccion aleatoria de simbiontes (d). Se utilizaron modelos lineales mixtos generalizados filogeneticos para analizar el efecto del tamano del parche, asi como los rasgos de tipo de crecimiento (crustaceo, folioso, frutal) y el modo de reproduccion (sexual frente a asexual) sobre la especializacion de los micobiontes. C_LIO_LITanto la riqueza de micobiontes como de fotobiontes a lo largo del gradiente de tamano de los parches siguio un patron de U inversa, que fue mas pronunciado en los fotobiontes. Los micobiontes que forman biotipos crustaceos establecieron el mayor numero de interacciones. La especializacion de los micobiontes (d) fue mayor para los biotipos fruticulosos y foliosos y para las especies con reproduccion vegetativa. A lo largo del gradiente del tamano del fragmento, el numero relativo de interacciones disminuyo y la especializacion de los micobiontes con reproduccion vegetativa aumento. C_LIO_LISintesis: El analisis de la especializacion de los micobiontes hacia sus fotobiontes en comunidades de liquenes epifitos en un bosque mediterraneo fragmentado revelo que no se puede descartar la interaccion entre los rasgos de vida de las especies y la perdida de habitat sobre la especializacion. Los resultados tambien apuntaron a la capacidad de algunas especies para modular sus interacciones hasta cierto punto, sugiriendo que las especies podrian tener una resiliencia a los cambios abioticos mayor de lo esperado, presumiblemente creando una deuda de extincion o incluso evitando los procesos de extincion hasta cierto punto. Palabras clave: Bosque mediterraneo, epifitos, fotobiontes, hongos liquenizados, selectividad. C_LI

ecology↗

bioRxiv2021

Accelerated decline of genome heterogeneity in the SARS-CoV-2 coronavirus

During the spread of the COVID-19 pandemic, the SARS-CoV-2 coronavirus underwent mutation and recombination events that altered its genome compositional structure, thus providing an unprecedented opportunity to search for adaptive evolutionary trends in real-time. The mutation rate in coronavirus is known to be lower than expected for neutral evolution, thus suggesting a role for natural selection. We summarize the compositional heterogeneity of each viral genome by computing its Sequence Compositional Complexity (SCC). To study the full range of SCC diversity, random samples of high-quality coronavirus genomes covering pandemic time span were analyzed. We then search for evolutionary trends that could inform on the adaptive process of the virus to its human host by computing the phylogenetic ridge regression of SCC against time (i.e., the collection date of each viral isolate). In early samples, we find no statistical support for any trend in SCC, although the viral genome appears to evolve faster than Brownian Motion (BM) expectation. However, in samples taken after the emergence of high fitness variants, and despite the brief time span elapsed, a driven decreasing trend for SCC, and an increasing one for its absolute evolutionary rate, are detected, pointing to a role for selection in the evolution of SCC in coronavirus genomes. We conclude that the higher fitness of variant genomes leads to adaptive trends of SCC over pandemic time in the coronavirus.

genomics↗

bioRxiv2020

Tracking evolutionary trends towards increasing complexity: a case study in Cyanobacteria

Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using six metrics of genome complexity, none of which is primarily associated to biological function, we measure genome complexity in 91 genomes from the phylum Cyanobacteria. Several phylogenetic analyses reveal the existence of progressive evolution towards higher genome complexity: 1) all the metrics detect strong phylogenetic signals; 2) ridge regressions detect positive trends towards higher complexity; and 3) classical proofs for progressive evolution (the minimum, the ancestor-descendent and the sub-clade tests), show that some of these positive trends are driven, being mainly due to natural selection. These findings support the existence of progressive genome evolution in this ancient and diverse group of organisms.

evolutionary biology↗