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Section: Ecology ; Topics: Ecology, Population biology, Statistics ; Conference: Euring 2023

Large-scale spatio-temporal variation in vital rates and population dynamics of an alpine bird

Nater, Chloé R.; Frassinelli, Francesco; Martin, James A.; Nilsen, Erlend B.

10.24072/pcjournal.494 - Peer Community Journal, Volume 4 (2024), article no. e111.
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Quantifying temporal and spatial variation in animal population size and demography is a central theme in ecological research and important for directing management and policy. However, this requires field sampling at large spatial extents and over long periods of time, which is not only prohibitively costly but often politically untenable. Participatory monitoring programs (also called citizen science programmes) can alleviate these constraints by recruiting stakeholders and the public to increase the spatial and temporal resolution of sampling effort and hence resulting data. While the majority of participatory monitoring programs are limited by opportunistic sampling designs, we are starting to see the emergence of structured citizen science programs that employ trained volunteers to collect data according to standardized protocols. Simultaneously, there is much ongoing development of statistical models that are increasingly more powerful and able to make more efficient use of field data. Integrated population models (IPMs), for example, are able to use multiple streams of data from different field monitoring programmes and/or multiple aspects of single datasets to estimate population sizes and key vital rates. Here, we developed a multi-area version of a recently developed integrated distance sampling model (IDSM) and applied it to data from a large-scale participatory monitoring program – the “Hønsefuglportalen” – to study spatio-temporal variation in population dynamics of willow ptarmigan (Lagopus lagopus) in Norway. We constructed an open and reproducible workflow for exploring temporal, spatial (latitudinal, longitudinal, altitudinal), and residual variation in recruitment, survival, and population density, as well as relationships between vital rates and relevant covariates and signals of density dependence. Recruitment rates varied more across space than over time, while the opposite was the case for survival. Slower life history patterns (higher survival, lower recruitment) appeared to be more common at higher latitudes and altitudes, portending differential effects of climate change on ptarmigan across their range. While there was variation in the magnitude of the effect small rodent occupancy had on recruitment, the relationships were predominantly positive and thus consistent with the alternative prey hypothesis. Notably, the accurate estimation of covariate effect was only made possible by integrating data from several monitoring areas for analysis. Our study highlights the potential of participatory monitoring and 2integrated modelling approaches for estimating and understanding spatio-temporal patterns in species abundance and demographic rates, and showcases how corresponding workflows can be set up in reproducible and semi-automated ways that increase their usefulness for informing management and regular reporting towards national and international biodiversity frameworks.
Section: Evolutionary Biology ; Topics: Ecology, Evolution, Genetics/genomics

A genomic duplication spanning multiple P450s contributes to insecticide resistance in the dengue mosquito Aedes aegypti

Bacot, Tiphaine; Haberkorn, Chloe; Guilliet, Joseph; Cattel, Julien; Kefi, Mary; Nadalin, Louis; Filee, Jonathan; Boyer, Frederic; Gaude, Thierry; Laporte, Frederic; Tutagata, Jordan; Vontas, John; Dusfour, Isabelle; Bonneville, Jean-Marc; David, Jean-Philippe

10.24072/pcjournal.497 - Peer Community Journal, Volume 4 (2024), article no. e110.
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Resistance of mosquitoes to insecticides is one example of rapid adaptation to anthropogenic selection pressures having a strong impact on human health and activities. Target-site modification and increased insecticide detoxification are the two main mechanisms underlying insecticide resistance in mosquitoes. While target-sites mutations are well characterised and often used to track resistance in the field, the genomic events associated with insecticide detoxification remain partially characterised. Recent studies evidenced the key role of gene duplications in the over-expression of detoxification enzymes and their potential use to track metabolic resistance alleles in the field. However, such genomic events remain difficult to characterise due to their complex genomic architecture and their co-occurrence with other resistance alleles. In this concern, the present work investigated the role of a large genomic duplication affecting a cluster of detoxification enzymes in conferring resistance to the pyrethroid insecticide deltamethrin in the mosquito Aedes aegypti. Two isofemale lines originating from French Guiana and being deprived from major target-site mutations showed distinct insecticide resistance levels. Combining RNA-seq and whole genome pool-seq identified a 220 Kb genomic duplication enhancing the expression of multiple contiguous cytochrome P450s in the resistant line. The genomic architecture of the duplicated loci was elucidated through long read sequencing, evidencing its transposon-mediated evolutionary origin. The involvement of this P450 duplication in deltamethrin survival was supported by a significant phenotypic response to the P450 inhibitor piperonyl butoxide together with genotype-phenotype association and RNA interference. Experimental evolution suggested that this P450 duplication is associated with a significant fitness cost, potentially affecting its adaptive value in presence of other resistance alleles. Overall, this study supports the importance of genomic duplications affecting detoxification enzymes in the rapid adaptation of mosquitoes to insecticides. Deciphering their genomic architecture provides new insights into the evolutionary processes underlying such rapid adaptation. Such findings provide new tools for the surveillance and management of resistance in the field.
Section: Genomics ; Topics: Genetics/genomics

Re-annotation of SARS-CoV-2 proteins using an HHpred-based approach opens new opportunities for a better understanding of this virus

Brézellec, Pierre

10.24072/pcjournal.496 - Peer Community Journal, Volume 4 (2024), article no. e109.
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Since the publication of the genome of SARS-CoV-2 – the causative agent of COVID-19 – in January 2020, many bioinformatic tools have been applied to annotate its proteins. Although effcient methods have been used, such as the identification of protein domains stored in Pfam, most of the proteins of this virus have no detectable homologous protein domains outside the viral taxa. As it is now well established that some viral proteins share similarities with proteins of their hosts, we decided to explore the hypothesis that this lack of homologies could be, at least in part, the result of the documented loss of sensitivity of Pfam Hidden Markov Models (HMMs) when searching for domains in "divergent organisms". In order to improve the annotation of SARS-CoV-2 proteins, we used the HHpred protein annotation tool. To avoid "false positive predictions" as much as possible, we designed a robustness procedure to evaluate the HHpred results. In total, 6 robust similarities involving 6 distinct SARS-CoV-2 proteins were detected. Of these 6 similarities, 3 are already known and well documented, and one is in agreement with recent crystallographic results. We then examined carefully the two similarities that have not yet been reported in the literature. We first show that the C-terminal part of Spike S (the protein that binds the virion to the cell membrane by interacting with the host receptor, triggering infection) has similarities with the human prominin-1/CD133; after reviewing what is known about prominin-1/CD133, we suggest that the C-terminal part of Spike S could both improve the docking of Spike S to ACE2 (the main cell entry receptor for SARS-CoV-2) and be involved in the delivery of virions to regions where ACE2 is located in cells. Secondly, we show that the SARS-CoV-2 ORF3a protein shares similarities with human G protein-coupled receptors (GPCRs), such as Lutropin-choriogonadotropic hormone receptor, primarily belonging to the "Rhodopsin family". To further investigate these similarities, we compared Prominin 1 and Lutropin-choriogonadotropic hormone receptor to a set of viral proteins using HHPRED. Interestingly, Prominin 1 showed similarities with 6 viral Spike glycoproteins, primarily from coronaviruses. Equally interestingly, Lutropin-choriogonadotropic hormone receptor showed similarities with 23 viral G-protein coupled receptors, particularly from Herpesvirales. We conclude that the approach described here (or similar approaches) opens up new avenues of research to better understand SARS-CoV-2 and could be used to complement virus annotations, particularly for less-studied viruses.
Section: Genomics ; Topics: Genetics/genomics

Chromosome-level genome reference of the Caucasian dwarf goby Knipowitschia cf. caucasica, a new alien Gobiidae invading the River Rhine

Schoenle, Alexandra; Guiglielmoni, Nadège; Mainz, Tobias; Greve, Carola; Hamadou, Alexander Ben; Heermann, Lisa; Borcherding, Jost; Waldvogel, Ann-Marie

10.24072/pcjournal.490 - Peer Community Journal, Volume 4 (2024), article no. e108.
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The Caucasian dwarf goby Knipowitschia cf. caucasica is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality chromosome-scale reference genome of Knipowitschia cf. caucasica by combining PacBio, Omni-C and Illumina technologies. The size of the assembled genome is 956.58 Mb with a N50 scaffold length of 43 Mb, which includes 92.3 % complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. 98.96 % of the assembly sequence was assigned to 23 chromosome-level scaffolds, with a GC-content of 42.83 %. Repetitive elements account for 53.08 % of the genome. The chromosome-level genome contained 26,404 transcripts with 23,210 multi-exons, of which 26,260 genes were functionally annotated. In summary, the high-quality genome assembly provides a fundamental basis to understand the adaptive advantage of the species.

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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA