Biology subjects

Larose, C.

Publications and source records attributed to Larose, C..

12 recordsLinked to original sources

bioRxiv2026

Environmental Correlates for Anticoagulant Resistance in house mice Mus musculus

Genetic resistance to anticoagulant rodenticides is a world-wide evolutionary phenomenon among invasive commensal rodents, that has not been investigated in Canada. We sequenced exon 3 of the VKORC1 gene of house mouse Mus musculus samples obtained from pest management professionals in Ontario and Quebec, to search for mutations known to confer resistance. Sanger sequencing was used alongside a novel qPCR assay for codons 128 and 139. We detected high prevalence (99%) of two non-synonymous single nucleotide polymorphisms in house mice, previously found in the USA and Europe, known to cause extreme resistance to first and some second-generation anticoagulants (L128S & Y139C). Homozygous resistant mice were more common in high population density areas. L128S alleles were more common in Southwestern Ontario, and Y139C in Central Ontario, despite high linkage disequilibrium. Detection success was far greater with qPCR than with Sanger sequencing. We conclude that uncoordinated rodenticide usage has selected for extreme resistance in mice throughout Ontario. Therefore, chemical control of the house mouse may be ineffective with first-generation anticoagulants throughout Ontario. This suggests that the evolution of wild urban mice is influenced by pest management practices, which may vary by region within the province.

evolutionary biology↗

bioRxiv2026

Brown and Lesser noddies as epidemiological reservoirs and sentinels of avian influenza virus in the South-western Indian Ocean

Avian influenza virus (AIV) epidemiology is well-documented in temperate regions but remains poorly understood in isolated ecosystems like tropical oceanic islands. On these islands, seabirds nest in dense interspecific colonies where the role of different species as reservoirs and dispersers of AIV may vary greatly. Here, we examine the role of noddies (Anous spp.) as potential reservoirs for low pathogenic AIV and evaluate their potential as sentinel species for highly pathogenic AIV introduction on tropical oceanic islands. We analyzed blood samples from 11 seabird species across eight islands in the southwestern Indian Ocean (2015-2020). Noddies exhibited high, stable seroprevalence (30-45%), comparable to reservoir host species in temperate regions. The detection of two N7-positive noddies, sampled the same year on two distinct islands, provided direct molecular evidence that AIV actively circulates on these island colonies. While most other species showed low exposure, Bridled Terns (Onychoprion anaethetus) had exceptionally high seroprevalence (80%), though their reservoir status requires further investigation due to limited sampling. Given noddies consistent exposure and regional distribution, we recommend prioritizing islands with large noddy populations for AIV surveillance. Continued investigation of viral dynamics within and among islands is now called for to elucidate the ecological drivers of AIV maintenance and transmission.

ecology↗

bioRxiv2023

Absence of Coronavirus in terns in the Western Indian Ocean?

We investigated coronavirus circulation in three tern species, in four islands of the Western Indian Ocean (Bird, Reunion, Europa, Juan de Nova). None of the 1513 samples tested positive by RT-PCR. We discuss the implication in term of host species range, ecological drivers of virus transmission, and diagnostic tools.

ecology↗

bioRxiv2023

Migratory patterns of two major influenza virus host species on tropical islands

Animal migration is a major driver of infectious agent dispersal. Duck and seabirds migrations, for instance, play a key role in the spatial transmission dynamics and gene flows of avian influenza viruses (AIV), worldwide. On tropical islands, brown and lesser noddies (Anous stolidus and A. tenuirostris) may be important AIV hosts, but the lack of knowledge on their migratory behaviour limits our understanding of virus circulation in island networks. Here we show that high connectivity between islands generated by post-breeding behaviours could be a major driver in the spread and the maintenance of AIV among tropical islands. Tracking data highlight two types of behaviours during the non-breeding season: birds either staying in the vicinity of their breeding ground (on Bird Island, Seychelles), or moving to and roosting on other islands in the Indian Ocean. Differences in roosting places are detected between migrant birds, ranging from the Tanzanian coast to the Maldives archipelago and Tromelin Island. Epidemiological data further support that brown and lesser noddies are major hosts for AIV, although significant variation of seroprevalence between species suggest that other drivers are involved in virus infection and transmission dynamics.

ecology↗

bioRxiv2022

EggVio: a user friendly and versatile pipeline for assembly and functional annotation of shallow depth sequenced samples

1We introduce a homemade pipeline allowing to improve the quality of the metagenomic annotations carried out when using shallow depth metagenomic datasets. The main motivation being to be able to quantify more precisely, with greater certainty, the genes involved in bacterial interactions. The limitation in our experimental design is that we use a sequencing technique with a low throughput (miSeq) compared to the metagenomic standard (hiSeq) because we carry out a fairly large sampling (almost a hundred samples) in time series. This methodological constraint from our study means that the assembly of the sequences is not very exhaustive (less than 50% of the sequences manage to be assembled). In this chapter, we will therefore present a new pipeline designed to specifically deal with such kind of data. We used co-assembly and a sequence annotation strategy in order to recover the sequences that could not be mapped on the assembled contigs. In addition, in order to avoid adding too much noise, when rescuing reads, we have built an algorithm to define a threshold of e-value based on the noise of the sequence annotation learned from sequences mapped in the assembly. We have selected several recent tools known to be effective for assembling, mapping and annotating these data. In addition, this pipeline was also built in order to be very user-friendly in terms of installation. In this idea of reproducibility, accessibility and transparency, we have designed an installation script to allow each user to install each tool required for the pipeline in a simple and reproducible way. Regarding the performances of this pipeline, we were able to show that the expected error rate (False discovery rate) for the annotation was close to 5%. Finally, we also used an actual dataset from a bioremediation site and showed that the representability of the samples seemed much better when we used our pipeline than when we used a classic metagenome assembly strategy.

microbiology↗

bioRxiv2022

Facultative parthenogenesis in an asexual stick insect: re-evolution of sex or vestigial sexual capacity?

Transitions from obligate sex to obligate parthenogenesis have occurred repeatedly across the tree of life. Whether these transitions occur abruptly or via a transient phase of facultative parthenogenesis is rarely known. We discovered and characterised facultatively parthenogenetic populations of the North American stick insect Timema douglasi, a species in which only obligately parthenogenetic populations were known so far. These populations comprised three genetic lineages. Females from all lineages were capable of parthenogenesis (with variable efficiency) but their propensity to reproduce sexually after mating varied extensively. In all three lineages, parthenogenesis resulted in the complete loss of heterozygosity in a single generation. Obligately parthenogenetic Timema have also lost all heterozygosity, suggesting that the transition to obligate parthenogenesis did not require a modification of the proximate mechanism, but rather involved a gradual increase in frequency. We speculate that facultative parthenogenesis may often be transient and be replaced by obligate strategies (either sex or parthenogenesis) because of a trade-off between the efficiency of the two reproductive modes. Such a trade-off could help explain why facultative parthenogenesis is rare among animals, despite its potential to combine the known benefits of sex and parthenogenesis.

evolutionary biology↗

bioRxiv2021

Micro-aggregation of a pristine grassland soil selects for bacterial and fungal communities and changes in nitrogen cycling potentials

Microbial analysis at the micro scale of soil is essential to the overall understanding of microbial organization and interactions, and necessary for a better understanding of soil ecosystem functioning. While bacterial communities have been extensively described, little is known about the organization of fungal communities as well as functional potentials at scales relevant to microbial interactions. Fungal and bacterial communities and changes in nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size sub-fractions (PSFs; > 250 m, 250-63 m, 63-20 m, 20-2 m, < 2 m and supernatant) were studied. The potential for nitrogen reduction was found elevated in bigger aggregates. The relative abundance of Basidiomycota deceased with decreasing particle size, Ascomycota showed an increase and Mucoromycota became more prominent in particles less than 20 m. Bacterial community structures changed below 20 m at the scale where microbes operate. Strikingly, only members of two bacterial and one fungal phyla (Proteobacteria, Bacteroidota and Ascomycota, respectively) were washed-off the soil during fractionation and accumulated in the supernatant fraction where most of the detected bacterial genera (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium and Variovorax) were previously associated with exopolysaccharide production and biofilm formation. Overall, the applied method shows potential to study soil microbial communities at micro scales which might be useful in studies focusing on the role of specific fungal taxa in soil structure formation as well as research on how and by whom biofilm-like structures are distributed and organized in soil. ImportanceIntensive exploitation of soils has led to increasing environmental concerns such as pollution, erosion, emission of greenhouse gases and, in general, the weakening of its ecosystem services that are mainly regulated by microbial activity. Microbial activity and metabolism drive the formation of soil aggregates, ranging in size from a few micrometres to several millimetres. Understanding biological mechanisms related to aggregate size classes can provide insight into large-scale processes, but most research has focused on macroaggregates. Here, we investigated the microbial community and its functional changes at these smaller scales that are clearly more relevant for assessing microbial activity. We demonstrated that fungal communities are more sensitive to bigger size classes than bacteria, suggesting their dominant role in soil structure formation and turnover. We also identified preferential niches for reductive processes within the nitrogen cycle and a selection of specific taxa by analysing the water used for the wet-fractionation approach.

ecology↗

bioRxiv2020

Snow Microbiome Functional Analyses Reveal Novel Microbial Metabolism of Complex Organic Compounds

Microbes active in extremely cold environments are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of twenty snow samples collected during early and late spring in Svalbard, Norway using our computational read-based microbiome function annotation tool, mi-faser. Our results revealed a more diverse microbiome functional capacity and activity in the early compared to in the late spring samples. The dissimilarity between the metagenomes and metatranscriptomes of the same samples was also significantly higher in the early spring. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant organisms, while late spring samples reflect a new community that is metabolically active. We additionally showed that the abundance of the sequencing reads mapping to the fatty acid synthesis-related microbial pathways was significantly positively correlated with organic acid levels, in both our late spring metagenomes and metatranscriptomes. Moreover, the geraniol degradation pathway and the styrene degradation pathway read abundances correlated and inversely correlated, respectively, with the organic acid levels. These results suggest a possible nutrient switch. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.

bioinformatics↗

bioRxiv2019

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome

BackgroundArctic surface soils experience pronounced seasonal changes in temperature and chemistry. However, it is unclear how these changes affect microbial degradation of organic matter, nitrogen cycling and microbial stress responses. We combined measurements of microbiome transcriptional activity, CO2 production, and pools of carbon and nitrogen to investigate the microbial response to warming in the laboratory, from -10 {degrees}C to 2 {degrees}C, and subsequent cooling, from 2 {degrees}C to -10 {degrees}C, of a high Arctic tundra soil from Svalbard, Norway.\n\nResultsGene expression was unaffected by warming from -10 {degrees}C to -2 {degrees}C and by cooling from -2 {degrees}C to -10 {degrees}C, while upon freezing (2 {degrees}C to -2 {degrees}C) a defense response against oxidative stress was observed. Following modest transcriptional changes one day after soil thaw, a more pronounced response was observed after 17 days, involving numerous functions dominated by an upregulation of genes involved in transcription, translation and chaperone activity. Transcripts related to carbohydrate metabolism and degradation of complex polymers (e.g. cellulose, hemicellulose and chitin) were also enhanced following 17 days of soil thaw, which was accompanied by a four-fold increase in CO2 production. In addition, anaerobic ammonium oxidation and turnover of organic nitrogen were upregulated. In contrast, nitrification, denitrification and assimilatory nitrate reduction were downregulated leading to an increase in the concentration of soil inorganic nitrogen.\n\nConclusionthe microorganisms showed negligible response to changes in sub-zero temperatures and a delayed response to thaw, which after 17 days led to upregulation of soil organic matter degradation and enhanced CO2 production, as well as downregulation of key pathways in nitrogen cycling and a concomitant accumulation of inorganic nitrogen available for plants.

microbiology↗

bioRxiv2018

Fundamental and realized feeding niche breadths of sexual and asexual stick-insects

The factors contributing to the maintenance of sex over asexuality in natural populations remain largely unknown. Ecological divergences between lineages with different reproductive modes could help to maintain reproductive polymorphisms, at least transiently, but there is little empirical information on the consequences of asexuality for the evolution of ecological niches. Here, we investigated how niche breadths evolve following transitions from sexual reproduction to asexuality. We estimated and compared the realized feeding niche breadths of five independently derived asexual Timema stick insect species and their sexual relatives. We found that asexual species had a systematically narrower realized niche than sexual species. To investigate how the narrower realized niches of asexual versus sexual species come about, we quantified the breadth of their fundamental niches but found no systematic differences between reproductive modes. The narrow realized niches found in asexuals are therefore likely a consequence of biotic interactions that constrain realized niche size in asexuals more strongly than in sexuals. Interestingly, the fundamental niche was broader in the oldest asexual species compared to its sexual relative. This broad ecological tolerance may help explain how this species has persisted over more than a million years in absence of sex.

ecology↗

bioRxiv2018

Evolutionary dynamics of specialization in herbivorous stick insects

Understanding the evolutionary dynamics underlying herbivorous insect mega-diversity requires investigating the ability of insects to shift and adapt to different host plants. Feeding experiments with nine related stick insect species revealed that insects retain the ability to use ancestral host plants after shifting to novel hosts, with host plant shifts generating fundamental feeding niche expansions. These expansions were not accompanied by expansions of the realized feeding niches however, as species on novel hosts are generally ecologically specialized. For shifts from angiosperm to chemically challenging conifer hosts, generalist fundamental feeding niches even evolved jointly with strong host plant specialization, indicating that host plant specialization is more likely driven by species interactions than by constraints imposed by plant chemistry. By coupling analyses of plant chemical compounds, fundamental and ecological feeding niches in multiple insect species, we provide novel insights into the evolutionary dynamics of host range expansion and contraction in herbivorous insects.

evolutionary biology↗

bioRxiv2018

Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing

DNA metabarcoding of faecal samples is being successfully used to study the foraging niche of species. We assessed the ability of two benchtop high-throughput sequencing (HTS) platforms, to identify a large taxonomic array of food items from domestic cats Felis silvestris catus, including prey and human-related food taxa (pet food and leftovers leaving undetectable solid remains in faeces). Scats from a captive feeding trial (n=41) and from free-ranging individuals (n=326) were collected and analysed using a cytb mini-barcode in independent PCR duplicates on the Ion PGM and the MiSeq platforms. Outputs from MiSeq were more sensitive and reproducible than those from Ion PGM due to a higher sequencing depth and sequence quality on MiSeq. DNA from intact prey taxa was detected more often (82% of the expected occurrences) than DNA from pet food (54%) and raw fish and meat (31%). We assumed that this variability was linked to different degree of DNA degradation: The Ion PGM detected significantly less human-linked food, birds, field voles, murids and shrews in the field-collected samples than the MiSeq platform. Pooling the replicates from both platforms and filtering the data allowed identification of at least one food item in 87.4% of the field-collected samples. Our DNA metabarcoding approach identified 29 prey taxa, of which 25 to species level (90% of items) including 9 rodents, 3 insectivores, 12 birds and 1 reptile and 33 human-related food taxa of which 23 were identified to genus level (75% of items). Our results demonstrate that using HTS platforms such as MiSeq, which provide reads of sufficiently high quantity and quality, with sufficient numbers of technical replicates, is a robust and non-invasive approach for further dietary studies on animals foraging on a wide range of food items in anthropogenic landscapes.

molecular biology↗