Latest Articles
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Section: Ecology ; Topics: Ecology
Spider mites collectively avoid plants with cadmium irrespective of their frequency or the presence of competitors
10.24072/pcjournal.435 - Peer Community Journal, Volume 4 (2024), article no. e64.
Get full text PDFAccumulation of heavy metals by plants can serve as a defence against herbivory. Herbivores, in turn, may avoid feeding on contaminated tissues. Such avoidance, however, may hinge upon the specific conditions faced by herbivores. Here, we tested whether the spider mite Tetranychus urticae avoids tomato plants contaminated with cadmium in presence of conspecifics or heterospecifics and depending on the frequency of contaminated plants. We show that individual spider mite females do not preferentially move to leaf tissues with or without cadmium, despite clear costs on their performance. However, in a set-up where 200 mites were simultaneously given the choice between four plants with or without cadmium, they collectively avoided plants with cadmium, irrespective of the proportion of plants with cadmium. In addition, T. urticae did not discriminate between plants infested with its competitor T. evansi and other uncontaminated plants but they preferred plants with competitors when the other plants contained cadmium. Our results show that aggregation may facilitate avoidance of contaminated plants. They also indicate that cadmium accumulation in plants is a stronger selective pressure than interspecific competition with T. evansi. Therefore, collective avoidance of metal-accumulating plants by herbivores is robust to environmental conditions and may have important consequences for species distribution and interactions in metal contaminated sites.
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Section: Genomics ; Topics: Genetics/genomics
T7 DNA polymerase treatment improves quantitative sequencing of both double-stranded and single-stranded DNA viruses
Billaud, Maud; Theodorou, Ilias; Lamy-Besnier, Quentin; Shah, Shiraz A.; Lecointe, François;
De Sordi, Luisa;
De Paepe, Marianne;
Petit, Marie-Agnès
10.24072/pcjournal.437 - Peer Community Journal, Volume 4 (2024), article no. e63.
Get full text PDFBulk microbiome, as well as virome-enriched shotgun sequencing only reveals the double-stranded DNA (dsDNA) content of a given sample, unless specific treatments are applied. However, genomes of viruses often consist of a circular single-stranded DNA (ssDNA) molecule. Pre-treatment and amplification of DNA using the multiple displacement amplification (MDA) method enables conversion of ssDNA to dsDNA, but this process can lead to over-representation of these circular ssDNA genomes. A more recent alternative permits to bypass the amplification step, as library adapters are ligated to sheared and denatured DNA, after an end-modification step (xGen kit). However, the sonication step might shear ssDNA more efficiently than dsDNA, therefore introducing another bias in virome sequencing. These limitations prompted us to explore an alternative method of DNA preparation for sequencing mixed ssDNA and dsDNA viromes. Using a synthetic mix of viral particles, we made use of the T7 DNA polymerase (T7pol) to convert viral circular ssDNA molecules to dsDNA, while preventing over-replication of such molecules, as is the case with the Phi29 DNA polymerase. Our findings indicate that using T7pol and a mix of degenerated primers to convert ssDNA to dsDNA prior library preparation is a good alternative to the currently used methods. It better represents the original synthetic mixtures compared to MDA or direct application of the xGen kit. Furthermore, when applied to two complex virome samples, the T7pol treatment improved both the richness and abundance in the Microviridae fraction. We conclude that T7pol pretreatment is preferable to MDA for the shotgun sequencing of viromes, which is easy to implement and inexpensive.
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Section: Ecology ; Topics: Ecology, Population biology, Statistics ; Conference: Euring 2023
Accounting for observation biases associated with counts of young when estimating fecundity: case study on the arboreal-nesting red kite (Milvus milvus)
10.24072/pcjournal.436 - Peer Community Journal, Volume 4 (2024), article no. e62.
Get full text PDFCounting the number of young in a brood from a distance is common practice, for example in tree-nesting birds. These counts can, however, suffer from over and undercounting, which can lead to biased estimates of fecundity (average number of nestlings per brood). Statistical model development to account for observation bias has focused on false negatives (undercounts), yet it has been shown that these models are sensitive to the presence of false positives (overcounts) when they are not accounted for. Here, we develop a model that estimates fecundity while accounting for both false positives and false negatives in brood counts. Its parameters can be estimated using a calibration approach that combines uncertain counts with certain ones, which can be obtained by accessing the brood, for example during ringing. The model uses multinomial distributions to estimate the probabilities of observing y young conditional on the true state of a brood z (i.e., true number of young) from paired uncertain and certain counts. These classification probabilities are then used to estimate the true state of broods for which only uncertain counts are available. We use a simulation study to investigate bias and precision of the model and parameterize the simulation with empirical data from 26 red kite nests visited with ground and nest-based counts during 2021 and 2022 in central Europe. In these data, bias in counts was at most 1 in either direction, more common in larger broods, and undercounting was more common than overcounting. This led to an overall 5% negative bias in fecundity in uncertain counts. The model produced essentially unbiased estimates (relative bias < 2%) of fecundity across a range of sample sizes. This held true whether or not fecundity was the same for nests with paired counts and those with uncertain-only counts. But the model could not estimate parameters when true states were missing from the paired data, which happened frequently in small sample sizes (n = 10 or 25). Further, we projected populations 50 years into the future using fecundity estimates corrected for observation biases from the multinomial model, and based on “raw” uncertain observations. We found that ignoring observation bias led to strong negative bias in projected population size for growing populations, but only minor negative bias in declining populations. Accounting for apparently minor biases associated with ground counts is important for ensuring accurate estimates of abundance and population dynamics especially for increasing populations. This could be particularly important for informing conservation decisions in projects aimed at recovering depleted populations.
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Section: Infections ; Topics: Biology of interactions, Ecology, Evolution
Differences in specificity, development time and virulence between two acanthocephalan parasites, infecting two cryptic species of Gammarus fossarum
Bauer, Alexandre;
Develay Nguyen, Lucie;
Motreuil, Sébastien;
Teixeira, Maria;
Debrosse, Nelly;
Rigaud, Thierry
10.24072/pcjournal.434 - Peer Community Journal, Volume 4 (2024), article no. e61.
Get full text PDFMulti-host parasites can exploit various host species that differ in abundance and susceptibility to infection, which will contribute unequally to their transmission and fitness. Several species of acanthocephalan manipulative parasites (among which Pomphorhynchus laevis and P. tereticollis) use various amphipod species of the genus Gammarus as intermediate hosts. Many Gammarus pulex and G. fossarum cryptic lineages are living in sympatry in European rivers, questioning the spectrum of intermediate hosts that acanthocephalans can use, and their relative contribution to their life cycles. In this work, the respective roles of parasites species (P. laevis and, for the first time, P. tereticollis) and sympatric host cryptic species (the G. fossarum species complex) were studied experimentally on two traits: host susceptibility to infection and parasite virulence. Differences were found, both in terms of infectivity and virulence, between the cryptic hosts and between the two parasite species. We confirm that these acanthocephalans, previously considered as generalists, show specificities among their sympatric hosts. Differences in field prevalence and susceptibility after experimental exposures were more pronounced between cryptic G. fossarum species for P. tereticollis than for P. laevis. The mortality of infected individuals increased significantly after several weeks of development of both parasite species. P. tereticollis was less virulent than P. laevis, perhaps due to differences in host exploitation, since we evidenced that P. tereticollis had a much slower growth rate.
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