Biology subjects

Almeida, P. R.

Publications and source records attributed to Almeida, P. R..

6 recordsLinked to original sources

bioRxiv2025

Population-specific bycatch risks in two vulnerable anadromous clupeids: insights from otolith microchemistry

Otolith microchemistry analysis revealed that bycatch of European shads--allis shad Alosa alosa (L. 1758) and twaite shad Alosa fallax (Lacepede 1803)-- in western Iberian commercial fisheries removes individuals from a wide array of natal origins, with the most abundant source rivers suffering the heaviest losses. Spatial variation in bycatch risk was evident: specific marine areas exhibited high natal-origin diversity, reflecting complex dispersal. A. alosa showed extensive medium- and long-distance movements-- including rare longitudinal displacements along the Cantabrian slope--and greater natal origin diversity than A. fallax, whose dispersal was largely restricted to middle-distance, latitudinal migrations. In both species, bycatches were dominated by the most abundant continental populations--Mondego and Minho for A. alosa, and Ulla and Minho for A. fallax--suggesting that these rivers function as source populations exporting individuals to sink populations through marine dispersal. Despite their differing dispersal ranges, both species displayed dual resident-dispersive contingents coexisting within the same populations, reflecting an interplay of river proximity, philopatry and resource availability. The stronger philopatry and constrained range of A. fallax imply heightened vulnerability to localized bycatch pressure near natal rivers, whereas A. alosas broader dispersal and higher origin diversity expose multiple populations to risk at a regional scale. These species-specific dispersal capacities and metapopulation structures critically shape bycatch vulnerability. Incorporating natal-origin and dispersal data into transnational, ecosystem-based management--such as targeted temporal or spatial fishing restrictions at mixing hotspots--will be essential to safeguard metapopulation dynamics, mitigate bycatch mortality, and maintain ecological connectivity among European shad populations.

ecology↗

bioRxiv2022

Seascape genomics reveals limited dispersal and suggest spatially varying selection among European populations of sea lamprey (Petromyzon marinus)

Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviours. Despite being a freshwater, free-living organism for large part of their life cycle, its adulthood is spent as a parasite of marine vertebrates. In their native European range, while it is well-established that sea lampreys comprise a single nearly-panmictic population, few studies have further explored the evolutionary history of natural populations. Here, we performed the first genome-wide characterization of sea lampreys genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase, with the sequencing 186 individuals from 8 locations spanning the North Eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30910 bi-allelic SNPs. Population genetic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the north eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species dispersal. Seascape genomics suggested a scenario where oxygen concentration and river runoffs impose spatially varying selection across their distribution range. Exploring associations with abundance of potential hosts further suggested that hake and cod could also impose selective pressures, although the nature of such putative biotic interactions was unresolved. Overall, the identification of adaptive seascapes in a panmictic anadromous species could contribute to conservation practices by providing information for restoration activities to mitigate local extinctions on freshwater sites. Sea lamprey Petromyzon marinus is an anadromous and semelparous fish without homing behaviours. Despite being a freshwater, free-living organism for large part of its life cycle, its adulthood is spent as a parasite of marine vertebrates. Here, we performed the first genome-wide characterization of sea lampreys genetic diversity in their European natural range. The objectives were to investigate the connectivity among river basins and explore evolutionary processes mediating dispersal during the marine phase. For that, we sequenced 186 individuals from 8 locations spanning the North-eastern Atlantic coast and the North Sea with double-digest RAD-sequencing, obtaining a total of 30910 bi-allelic SNPs. Population genomic analyses reinforced the existence of a single metapopulation encompassing freshwater spawning sites within the north-eastern Atlantic and the North Sea, though the prevalence of private alleles at northern latitudes suggested some limits to the species dispersal. Seascape analyses revealed candidate loci associated with the abundance of some host species and were located in a genomic region coding for variable lymphocyte receptors, an adaptive immunity tool unique to jawless vertebrates, and to MARCH proteins, a family of E3 ubiquitin ligases also involved in the regulation of immune responses. Abiotic factors (e.g., maximum phosphate, dissolved oxygen and water temperature) were significantly correlated with candidate loci associated with the myo-inositol synthesis, a pathway linked to osmoregulation, and to other genomic regions involved in organismal homeostasis. The identification of adaptive seascapes in this ancient species, especially if linked to primitive adaptive immune responses, could be relevant to understand the evolutionary pathways early in vertebrate evolution.

evolutionary biology↗

bioRxiv2022

Widespread hybridization between invasive bleak (Alburnus alburnus) and native Iberian chubs (Squalius spp.): a neglected threat

Hybridization between native and exotic species is a major conservation issue. In Iberian rivers, which are simultaneously among the most invaded and diverse ecosystems, harboring a high proportion of endemic fishes, this issue is becoming highly concerning. To date, hybridization has been reported to occur between the invasive bleak Alburnus alburnus and the endemic chubs Squalius alburnoides and S. pyrenaicus, in some scattered locations. However, the bleak is increasingly spreading in the region, potentially increasing the risks of hybridization with these and other Squalius species. To gather a more comprehensive picture on the current extension of hybridization, we compiled and mapped records on hybrids between bleak and chubs collected by multiple research teams in different ongoing projects in the Portuguese territory, and genetically assessed the hybrid identity of specimens in an area of sympatry between bleak and S. carolitertii, using nuclear and mitochondrial markers. We found that hybridization with bleak is widespread in several Portuguese river basins and involves at least three endemic chubs, S. alburnoides, S. pyrenaicus and S. carolitertii. This may have serious consequences, including not only waste of reproductive effort and damage of genetic integrity, but also putative shifts on the reproductive dynamics of the Squalius system, which includes endemic hybrids, reproducing sexually and nonsexually. Hybridization should be recognized as a significant impact of biological invasions, and we recommend that future studies should characterize the fitness of hybrids and their ecological and genetic interactions with parental Iberian fish, to elucidate effective conservation measures.

zoology↗

bioRxiv2020

SARS-CoV2 quantification using RT-dPCR: a faster and safer alternative to assist viral genomic copies assessment using RT-qPCR

In this study, serial dilutions of SARS-CoV 2 RNA extract were tested using RT-dPCR using three different primer-probe assays aiming SARS-CoV 2 nucleocapsid coding region. Narrower confidence intervals, indicating high quantification precision were obtained in 100 and 1000-fold serial dilution and RT-dPCR results were equivalent between different assays in the same dilution. High accuracy of this test allowed conclusions regarding the ability of this technique to evaluate precisely the amount of genomic copies present in a sample. We believe that this fast and safe method can assist other researchers in titration of SARS-CoV2 controls used in RT-qPCR without the need of virus isolation.

molecular biology↗

bioRxiv2019

Detection of a novel African-lineage-like Zika virus naturally infecting free-living neotropical primates in Southern Brazil

Mosquito borne flaviviruses cause a series of important diseases in humans and animals. These viruses are maintained in cycles involving replication in mosquito and in vertebrate hosts. Most natural hosts are vertebrate animals living in sylvatic or peridomestic environments. Human contact with these environments may result in host shifts that lead to the establishment of urban transmission cycles. Zika virus is a Flavivirus that persists in nature in a transmission cycle involving non-human primates (NHP). Its recent emergence in Brazil has shed light upon the importance of surveying this agent in Brazilian sylvatic environments. Here we present histopathological and molecular evidence that free ranging howler monkeys (Alouatta guariba) in Southern Brazil are infected by ZIKV closely related to African lineage MR766. Nine NHP were nested RT-PCR positive for ZIKV RNA. Sequence analysis revealed 96 to 98% identity to ZIKV MR766 and 85% identity to ZIKV P6-740, the current epidemic strain. The affected howler monkeys presented discrete inflammatory infiltrates in several tissues and immunohistochemichal (IHC) labeling of viral antigen was observed in placenta. These findings point to the circulation of African lineage Zika virus in the Americas in non-human primates. And raises the possibility that ZIKV was introduced into the Americas on more than one occasion.

microbiology↗

bioRxiv2018

Disentangling the Role of Face Typicality and Affect in Emotional Face Processing: Self-reported and Electrophysiological Evidence

Typicality, or averageness, is one of the key features that influences face evaluation, but the role of this property in the perception of facial expressions of emotions is still not fully understood. Typical faces are usually considered more pleasant and trustworthy, and neuroimaging results suggest typicality modulates amygdala and fusiform activation, influencing face perception. At the same time, there is evidence that arousal is a key affective feature that modulates neural reactivity to emotional expressions. In this sense, it remains unclear whether the neural effects of typicality depend on altered perceptions of affect from facial expressions or if the effects of typicality and affect independently modulate face processing. The goal of this work was to dissociate the effects of typicality and affective properties, namely valence and arousal, in electrophysiological responses and self-reported ratings across several facial expressions of emotion. Two ERP components relevant for face processing were measured, the N170 and Vertex Positive Potential (VPP), complemented by subjective ratings of typicality, valence, and arousal, in a sample of 30 healthy young adults (21 female). The results point out to a modulation of the electrophysiological responses by arousal, regardless of the typicality or valence properties of the face. These findings suggest that previous findings of neural responses to typicality may be better explained by accounting for the subjective perception of arousal in facial expressions.

neuroscience↗