Biology subjects

Piris, A.

Publications and source records attributed to Piris, A..

3 recordsLinked to original sources

bioRxiv2026

Resurvey of boreal earthworm communities in southern and northern Finland

In northern boreal Europe, the Last Glaciation Maximum resulted in a tabula rasa of earthworm species, post-glacial recolonisation of few peregrine species. Boreal forests represent 11.5% of the Earth's land area, and their cold winters represent the harshest season for earthworms. These biotopes are subject to substantial global changes, notably climate change and land use intensification, which might impact earthworm populations. Yet, no study measuring temporal changes in earthworm population or diversity is known in this biotope. Here, we sampled earthworm communities in two northern and two southern areas in Finland forests. In total, 21 sites were surveyed in 2015 and resurveyed 10 years later in 2025-2026. We aimed at understanding how earthworm diversity and populations changed in the last 10 years, comparing community and species-specific diversity metrics. In ten years, although not significant, earthworm abundance declined (-20%), whereas richness increased (+13%). The cold-tolerant Dendrobaena octaedra decreased, being the only one with a significant change. Temporal community and species dynamics followed a south-north gradient. Southern sites showed a decrease in abundance and D. octaedra populations, with an increase in abundance and occupancy of more heat-tolerant species. Northern sites showed an increase in abundance uniquely due to an increase in D. octaedra populations, but no other species were found there. These changes can be linked to climate changes leading to less rigorous winters in both south and north of Finland, and more rigorous summers in the south, potentially interacting with intense forest management, but could also be attributed to a still ongoing post-glacial recolonisation. These results call for more long-term sampling of earthworm communities in these fragile and rapidly changing environments.

ecology↗

bioRxiv2023

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genus Cerastes

The desert vipers of the genus Cerastes are a small clade of medically important venomous snakes within the family Viperidae. According to published morphological and molecular studies, the group is comprised by four species: two morphologically similar and phylogenetically sister taxa, the African horned viper (Cerastes cerastes) and the Arabian horned viper (Cerastes gasperettii); a more distantly related species, the Saharan sand viper (Cerastes vipera), and the enigmatic Bohmes sand viper (Cerastes boehmei), only known from a single specimen in captivity allegedly captured in Central Tunisia. In this study, we analyzed one mitochondrial marker (COI) as well as genome-wide data (ddRAD sequencing) from 28 and 41 samples, respectively, covering the entire distribution range of the genus to explore the population genomics, phylogenomic relationships and introgression patterns within the genus Cerastes. Additionally, and to provide insights into the mode of diversification of the group, we carried out niche overlap analyses considering climatic and habitat variables. Both nuclear phylogenomic reconstructions and population structure analyses have unveiled an unexpected evolutionary history for the genus Cerastes, which sharply contradicts the morphological similarities and previously published mitochondrial approaches. Cerastes cerastes and C. vipera are recovered as sister taxa whilst C. gasperettii is a sister taxon to the clade formed by these two species. We found a relatively high niche overlap (OI > 0.7) in both climatic and habitat variables between C. cerastes and C. vipera, contradicting a potential scenario of sympatric speciation. These results are in line with the introgression found between the northwestern African populations of C. cerastes and C. vipera. Finally, our genomic data confirms the existence of a lineage of C. cerastes in Arabia. All these results highlight the importance of genome-wide data over few genetic markers to study the evolutionary history of species.

genomics↗

bioRxiv2019

Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma

Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin mediated by the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultraviolet induced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep sequencing studies of MCC have identified significant differences between the number and types of point mutations, copy number alterations, and structural variants between virus-positive and virus-negative tumors. In this study, we assembled a cohort of 71 MCC patients and performed deep sequencing with OncoPanel, a next-generation sequencing assay targeting over 400 cancer-associated genes. To improve the accuracy and sensitivity for virus detection compared to traditional PCR and IHC methods, we developed a hybrid capture baitset against the entire MCPyV genome. The viral baitset identified integration junctions in the tumor genome and generated assemblies that strongly support a model of a hybrid, virus-host, circular DNA intermediate during integration that promotes focal amplification of host DNA. Using the clear delineation between virus-positive and virus-negative tumors from this method, we identified recurrent somatic alterations common across MCC and alterations specific to each class of tumor, associated with differences in overall survival. Comparing the molecular and clinical data from these patients revealed a surprising association of immunosuppression with virus-negative MCC and significantly shortened overall survival. These results demonstrate the value of high-confidence virus detection for identifying clinically important features in MCC that impact patient outcome.

cancer biology↗