Biology subjects

Valerio, F.

Publications and source records attributed to Valerio, F..

6 recordsLinked to original sources

bioRxiv2025

Progress in the molecular Phylogeny of Cotesia acuminata and C. melitaearum cryptic species complexes

Cryptic species present major challenges for biodiversity and evolutionary research due to the morphological similarity and frequent lack of genetic and ecological data. In parasitoids wasps, this is especially true for lineages with limited sampling and unclear species boundaries. Here we reconstruct the phylogeny of Cotesia wasps parasitizing Melitaeini butterflies, including two cryptic species complexes (Cotesia acuminata agg. and C. melitaearum agg.). Using a ten-gene dataset from samples collected in Europe, Asia, and North America, we inferred relationships among 22 Cotesia species using maximum likelihood. We also included non-Melitaeini associated Cotesia to assess whether the Melitaeini parasitoids form a monophyletic group. Our analyses yielded a highly supported phylogeny, revealing four major clades, three of which included the Melitaeini associated species. This confirms that the Cotesia attacking Melitaeini butterflies are polyphyletic, resulting from independent host shifts across the genus. Each clade is further subdivided into subclades corresponding to the different (cryptic) species, clarifying previously unresolved relationships. These results provide a robust framework for future studies on the evolution, ecology, and host use dynamics of Cotesia wasps and highlight the utility of multi-locus data for resolving phylogenies in morphologically cryptic taxa.

evolutionary biology↗

bioRxiv2024

Multi-Temporal Remote Sensing of Inland Surface Waters: A Fusion of Sentinel-1 Data Applied to Small Seasonal Ponds in Semiarid Environments

Inland freshwater resources in semiarid environments play a key role in maintaining ecological systems and supporting human development. Space-based remote sensing spatiotemporal data have emerged as a new paradigm for understanding ecohydrological processes and trends, particularly in water-stressed areas. However, comprehensive cataloging is still lacking, especially in semi-arid regions and for small-sized water bodies (i.e., ponds), which are often overlooked despite their ecological relevance. In this study, high-resolution optical and radar Sentinel data (Sentinel-1 and Sentinel-2) were used to construct Sentinel-1&2-based local surface water (SLSW) models, to infer surface water occurrence and extent. To assess the reliability of this model, the results were compared with verification data, and separately with Landsat-based global water (LGSW) models. Three distinct semiarid regions were selected in SW Iberia, within a Mediterranean climate, each encompassing special protection areas for conservation and subjected to marked seasonality and bioclimatic changes. Surface water attributes were modeled using Random Forests for SLSW time series forecasting, which included the period from January 1, 2020, to December 31, 2021. During this period, the completeness of the archived information was compared between SLSW and LGSW, considering both intra-annual and inter-annual variations. The predictive performance of these models was then compared for specific periods (dry and wet), and each was independently validated with verification data. The results showed that SLWM achieved satisfactory predictive performances in detecting surface water occurrence ({approx}72%), with far greater completeness and reconstructed seasonality patterns compared to LGSW. The relatedness between SLSW and LGSW was stronger during wet periods (R2=0.38) than dry periods (R2=0.05), and SLSW related much better with the verification data (R2=0.66) than when compared to LGSW (R2=0.24). The proposed SLSW approach may therefore provide advantages in the delineation of dynamic surface water characteristics (occurrence and extent) in very small-sized water bodies (i.e., <0.5 ha), allowing for uninterrupted surface water time series forecasting at high spatiotemporal detail, and over extensive areas. Given the water constraints in semiarid regions and water resources vulnerability to climate change, our results show high potential for supporting a variety of activities underlying rural development and biodiversity conservation. Additionally, the socio-ecological applications of this research may help identify surface water anomalies (e.g., drought events) and enhance sustainable water supply governance, a particular priority in climate change hotspots. HighlightsO_LISurface water occurrence and extent was modeled across three semiarid regions C_LIO_LISentinel-1&2 data was compared with Landsat for characterizing very small water bodies C_LIO_LIModels based on Sentinel-1&2 resulted in a satisfactory classification precision C_LIO_LIVery high series completeness across seasons was found using Sentinel-1&2 data C_LIO_LISentinel-1&2 data was more reliable than Landsat when compared to verification data C_LI

ecology↗

bioRxiv2021

The impact of fast radiation on the phylogeny of Bactrocera fruit flies

True fruit flies (Tephritidae) include several species that cause extensive damage to agriculture worldwide. Among them, species of the genus Bactrocera are widely studied to understand the traits associated to their invasiveness and ecology. Comparative approaches based on a reliable phylogenetic framework are particularly effective, but, to date, molecular phylogenies of Bactrocera are still controversial. Here, we employed a comprehensive genomic dataset to infer a robust backbone phylogeny of eleven representative Bactrocera species and two outgroups. We further provide the first genome scaled inference of their divergence using calibrated relaxed clock. The results of our analyses support a closer relationship of B. dorsalis to B. latifrons than to B. tryoni, in contrast to all mitochondrial-based phylogenies. By comparing different evolutionary models, we show that this incongruence likely derives from the fast and recent radiation of these species that occurred around 2 million years ago, which may be associated with incomplete lineage sorting and possibly (ongoing) hybridization. These results can serve as basis for future comparative analyses and highlight the utility of using large datasets and efficient phylogenetic approaches to study the evolutionary history of species of economic importance.

evolutionary biology↗

bioRxiv2019

Polymorphism analyses and protein modelling inform on functional specialization of Piwi clade genes in the arboviral vector Aedes albopictus

Current knowledge of the piRNA pathway is based mainly on studies on the model organism Drosophila melanogaster, where three proteins of the Piwi subclade of the Argonaute family interact with PIWI-interacting RNAs to silence transposable elements in gonadal tissues. In mosquito species that transmit epidemic arboviruses such as the Dengue and Chikungunya viruses, Piwi clade genes underwent expansion, are also expressed in the soma, and code for proteins that may elicit antiviral functions and crosstalk with other proteins of recognized antiviral mechanisms. These observations underline the importance of expanding our knowledge of the piRNA pathway beyond D. melanogaster.\n\nHere we focus on the emerging arboviral vector Aedes albopictus and we couple traditional approaches of expression and adaptive evolution analyses with most current computational predictions of protein structure to study evolutionary divergence among Piwi clade proteins. Superposition of protein homology models indicate high structure similarity among all Piwi proteins, with high levels of amino acid conservation in the inner regions devoted to RNA binding. On the contrary, solvent-exposed surfaces showed low conservation, with several sites under positive selection. Expression profiles of Piwi transcripts during mosquito development and after infection with the Dengue 1 virus showed a concerted elicitation of all Piwi transcripts during viral dissemination, while the maintenance of infection primarily relied on the expression of Piwi5. In contrast, establishment of persistent infection by the Chikungunya virus is accompanied by an increased expression of all Piwi genes, particularly Piwi4 and, again, Piwi5. Overall these results are consistent with functional specialization and a general antiviral role for Piwi5. Experimental evidences of sites under positive selection in Piwi1/3, Piwi4 and Piwi6, further provide useful knowledge to design tailored functional experiments.\n\nAuthor summaryArgonautes are ancient proteins involved in many cellular processes, including innate immunity. Early in eukaryote evolution, Argonautes separated into Ago and Piwi clades, which maintain a dynamic evolutionary history with frequent duplications and losses. The use of Drosophila melanogaster as a model organism proved fundamental to understand the function of Argonautes. However, recent studies showed that the patterns and observations made in D. melanogaster, including the number of Argonautes, their expression profile and their function, are a rarity among Dipterans.\n\nIn vectors of epidemic arboviruses such as Dengue and Chikungunya viruses, Piwi genes underwent expansion, are expressed in the soma, and some of them appear to have antiviral functions. Besides being an important basic question, the identification of which (and how) Piwi genes have antiviral functions may be used for the development of novel genetic-based strategies of vector control. Here we coupled population genetics models with computational predictions of protein structure and expression analyses to investigate the evolution and function of Piwi genes of the emerging vector Aedes albopictus. Our data support a general antiviral role for Piwi5. Instead, the detection of complex expression profiles with the presence of sites under positive selection in Piwi1/3, Piwi4 and Piwi6 requires tailored functional experiments to clarify their antiviral role.

evolutionary biology↗

bioRxiv2019

Integrated RNA and metabolite profiling of urine liquid biopsies for prostate cancer biomarker discovery

Sensitive and specific diagnostic and prognostic biomarkers for prostate cancer (PCa) are urgently needed. Urine samples are a non-invasive means to obtain abundant and readily accessible \"liquid biopsies\". Herein we used urine liquid biopsies to identify and characterize a novel group of urine-enriched RNAs and metabolites in PCa patients and normal individuals with or without benign prostatic disease. Differentially expressed RNAs were identified in urine samples by deep sequencing and metabolites in urine were measured by mass spectrometry. The mRNA and metabolite profiles were distinct in patients with benign and malignant disease. Integrated analysis of urinary gene expression and metabolite signatures unveiled an aberrant glutamate metabolism and tricarboxylic acid (TCA) cycle node in prostate cancer-derived cells. Functional validation supports a role for glutamate metabolism and glutamate oxaloacetate transaminase 1 (GOT1)-dependent redox balance in prostate cancer, which can be exploited for novel biomarkers and therapies.

cancer biology↗

bioRxiv2018

Evolutionary landscape of mosquito viral integrations

The sequenced genome of the arboviral vector mosquito, Aedes albopictus, is replete with repetitive DNA and it harbors an unusually large number of endogenous viral sequences, collectively called Nonretroviral Integrated RNA Virus Sequences (NIRVS). NIRVS are enriched both within protein-coding gene exons and PIWI-interacting RNA (piRNA) clusters, where they encode piRNAs. Based on these features, NIRVS have been proposed to function as novel mosquito antiviral immune factors. However, the relative importance and contributions of different NIRVS as functional antiviral elements and their mechanisms of action remain open questions.\n\nWe apply an analytical approach that intersects computational, evolutionary and molecular methods to identify NIRVS most likely affecting mosquito immunity. Using this strategy, we show that NIRVS are a highly dynamic component of the Ae. albopictus repeatome, which nevertheless maintains a core set of seemingly the oldest NIRVS with similarity to Rhabdoviruses. Population-level polymorphism of NIRVS varies depending on whether they occur in intergenic regions, piRNA clusters or are part of gene exons. NIRVS from piRNA clusters are differentially widespread in diverse populations but conserved at the sequence level. This is consistent with the hypothesis that they act analogously to fragments of transposable elements in piRNA clusters and contribute to piRNA-based immunity. Among NIRVS from gene exons, AlbRha52 and AlbRha12 have the hallmarks of domestication as they are fixed across populations, stably expressed, and as polymorphic at the sequence level as fast-evolving genes. Overall these results support the hypothesis that NIRVS contribute to mosquito immunity, potentially through diverse modes of action.

evolutionary biology↗