Biology subjects

Cottenie, K.

Publications and source records attributed to Cottenie, K..

8 recordsLinked to original sources

bioRxiv2026

Biological implications of a detailed repeat annotation in Octopus vulgaris

Octopuses are phenotypically distinctive organisms, and recent genomic work raises questions about the contributions of transposable elements (TE) to their genomic architecture. We leveraged a robust repeat annotation pipeline, in combination with manual and automated curatorial techniques, to produce a more comprehensive repeat annotation of Octopus vulgaris. This revealed that [~]66% of the genome are repeats, in contrast to previous estimates of 43-50%. Whereas previous studies of TE expansion in Octopus bimaculoides identified two bursts of activity, 25 and 56 MYA, our re-annotation revealed four such expansions at 18, 25, 33, and 56 MYA. We further identified a landscape of TE hot- and cold spots. This much refined TE timescape and landscape will serve as a useful basis for understanding TE contributions to O. vulgaris evolution, and also for identifying factors contributing to variation in the TE community across genomic space and evolutionary time.

genomics↗

bioRxiv2023

Novel Pipeline for Large-Scale Comparative Population Genetics

As scientists continue to ask complex questions about biodiversity and deal with increasingly large amounts of data, there is a demand for new methods and computational developments to perform scientific analyses. Analytical pipelines and modules can provide a way to meet these demands and ensure reproducibility in scientific methods and analyses. The goal of this study was to create efficient, reproducible, reusable programming modules that are publicly available for future research. These modules were used to determine population genetic structure measures and compare these measures across species with different biological traits. The functionality of the modules is shown through a case study on Diptera (true fly) species from Canada and Greenland. We leveraged high-throughput DNA sequencing data from Northern areas, as it is a valuable resource and provides new opportunities to study the Arctic. Data were pulled from public databases (Barcode of Life Data System and Global Biodiversity Information Facility), as well as taxon-specific literature. The pipeline we developed in R includes fifteen modules, including modules to prepare and filter the data, calculate population genetic structure measures (e.g., FST), and run a multiple regression. These modules can be easily adapted and applied to a diverse set of animal groups, geographic regions, and biological traits. Best practices were followed for pipeline development, and the modules were designed and tested to work for datasets of different sizes by providing multiple different analyses and filtering options. Biological results were also obtained for Diptera species. Habitat and larval diet were both significantly related to population genetic structure. Evidence of isolation by distance and a relationship between population genetic structure and both latitude and longitude were also found. Overall, this study has created efficient, reusable bioinformatics modules, and provided insight into the factors affecting population genetic structure in Northern fly communities.

bioinformatics↗

bioRxiv2022

Metabarcoding metacommunities: time, space, and land use interact to structure aquatic macroinvertebrate communities in streams

There is an increasing need to move beyond evaluating the effect of land use on stream communities by only studying local variables, and instead incorporate a metacommunity perspective which integrates environmental and spatial factors across larger spatial scales. The use of molecular tools (DNA metabarcoding) to identify bioindicator groups, such as aquatic macroinvertebrates, can provide greater taxonomic resolution to explore patterns in stream metacommunities. In this study, we collected aquatic macroinvertebrates from streams in southern Ontario which spanned a gradient of agricultural disturbance and used DNA metabarcoding to identify the species composition from these samples. We address a significant knowledge gap in previous stream aquatic macroinvertebrate metacommunity studies by incorporating molecular identification as well as a temporal component. We observed that a combination of local habitat conditions, regional agricultural land use, and spatial position influenced aquatic macroinvertebrate community composition, suggesting there is an interaction between environmental filtering and dispersal processes that structures these communities. However, aquatic macroinvertebrate communities were also highly dissimilar between streams and composed of many rare species, and a large percentage of unexplained variation suggests that there is a strong stochastic component to community assembly. We also observed that there is a seasonal component to metacommunity dynamics, with different water quality variables being significant to community composition in each sampling month. While we expected that an increased percentage of surrounding agricultural land use would result in more homogenous macroinvertebrate communities, we only detected this relationship in May and found evidence that a larger riparian buffer width can mitigate the effects of agricultural land use. We demonstrate the utility of DNA metabarcoding for revealing patterns in metacommunity dynamics that may not be detectable using coarse taxonomic identifications, and reveal the importance of incorporating a seasonal component when evaluating the influence of land use on community composition.

ecology↗

bioRxiv2022

Hidden diversity - DNA metabarcoding reveals hyper-diverse benthic invertebrate communities

Freshwater ecosystems, such as streams, are facing increasing pressures from agricultural land use. Aquatic insects and other macroinvertebrates have historically been used as indicators of ecological condition and water quality in freshwater biomonitoring programs; however, many of these protocols use coarse taxonomic resolution (e.g., family) when identifying macroinvertebrates. The use of family-level identification can mask species-level diversity, as well as patterns in community composition in response to environmental variables. Recent literature stresses the importance of robust biomonitoring to detect trends in insect decline globally, though most of these studies are carried out in terrestrial habitats. Here, we incorporate molecular identification (DNA metabarcoding) into a stream biomonitoring sampling design to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales. We sampled twenty southern Ontario streams in an agricultural landscape for aquatic macroinvertebrates and, using DNA metabarcoding, revealed incredibly rich benthic communities which were largely comprised of rare taxa detected only once per stream despite multiple biological replicates. In addition to numerous rare taxa, our species pool estimates indicated that after 240 samples from twenty streams, there was a large proportion of taxa present which remained undetected by our sampling regime. When comparing different levels of taxonomic resolution, we observed that using OTUs revealed over ten times more taxa than family-level identification. A single insect family, the Chironomidae, contained over one third of the total number of OTUs detected in our study. Within-stream dissimilarity estimates were consistently high for all taxonomic groups (invertebrate families, invertebrate OTUs, chironomid OTUs), indicating stream communities are very dissimilar at small spatial scales. While we predicted that increased land use would homogenize benthic communities, this was not supported as within-stream dissimilarity was unrelated to land use.

ecology↗

bioRxiv2020

At each site its diversity: DNA barcoding reveals remarkable earthworm diversity in neotropical rainforests of French Guiana

Despite their recognized essential role in soil, earthworms in tropical environments are still understudied. The aim of this study was to re-evaluate the diversity at the regional scale, as well as to investigate the environmental and spatial drivers of earthworm communities. We sampled earthworm communities across a range of habitats at six locations in French Guiana using three different sampling methods. We generated 1675 DNA barcodes and combined them with data from a previous study. Together, all sequences clustered into 119 MOTUs which were used as proxy to assess species richness. Only two MOTUs were common between the six locations and 20.2 % were singletons, showing very high regional species richness and a high number of rare species. A canonical redundancy analysis was used to identify key drivers of the earthworm community composition. The RDA results and beta-diversity calculations both show strong species turnover and a strong spatial effect, resulting from dispersal limitations that are responsible for the current community composition. Sampling in different microhabitats allowed the discovery of 23 MOTUs that are exclusively found in decaying trunks and epiphytes, highlighting hidden diversity of earthworms outside of soil.

ecology↗

bioRxiv2020

Examining interspecific density-dependent dispersal in forest small mammals

The effects of conspecific densities on dispersal have been well documented. However, while positive and negative density-dependent dispersal based on conspecific densities are often shown to be the result of intraspecific competition or facilitation respectively, the effects of heterospecific densities on dispersal are examined far less frequently. This despite the potential for the analogous processes of interspecific competition and heterospecific attraction to influence dispersal. Here we use 51 years of live-trapping data on deer mouse (Peromsycus maniculatus), eastern chipmunk (Tamias striatus), red-backed vole (Myodes gapperi), and jumping mice (Napaeozapus insignis and Zapus hudsonius) to examine the effects of both conspecific and heterospecific densities on dispersal frequency. In terms of conspecific densities, jumping mice were more likely to disperse from areas of low conspecific densities, while red-backed voles and chipmunks did not respond to conspecific densities in their dispersal frequencies. When considering interspecific density effects, while there were no statistically clear effects of density on dispersal frequency, the effects of chipmunk and jumping mice densities on dispersal by red-backed vole were greater than the effects of conspecific densities, with voles more likely to disperse from areas of high chipmunk densities and low jumping mice densities. Likewise, the effect of chipmunk densities on dispersal by jumping mice was greater than the conspecific density effect. Conspecific densities clearly can affect dispersal by two of these four species, but the effects of heterospecific densities on dispersal frequency are less clear. Based on effect sizes it appears that there is potential for heterospecific effects on dispersal by some species in the community, but future experimental work could elucidate the strength and causes of these relationships.

ecology↗

bioRxiv2019

Genomic Environments and Their Influence on Transposable Element Communities

BackgroundDespite decades of research the factors that cause differences in transposable element (TE) distribution and abundance within and between genomes are still unclear. Transposon Ecology is a new field of TE research that promises to aid our understanding of this often-large part of the genome by treating TEs as species within their genomic environment, allowing the use of methods from ecology on genomic TE data. Community ecology methods are particularly well suited for application to TEs as they commonly ask questions about how diversity and abundance of a community of species is determined by the local environment of that community.\n\nResultsUsing a redundancy analysis, we found that ~ 50% of the TEs within a diverse set of genomes are distributed in a predictable pattern along the chromosome, and the specific TE superfamilies that show these patterns are relate to the phylogeny of the host taxa. In a more focused analysis, we found that ~60% of the variation in the TE community within the human genome is explained by its location along the chromosome, and of that variation two thirds (~40% total) was explained by the 3D location of that TE community within the genome (i.e. what other strands of DNA physically close in the nucleus). Of the variation explained by 3D location half (20% total) was explained by the type of regulatory environment (sub compartment) that TE community was located in. Using an analysis to find indicator species, we found that some TEs could be used as predictors of the environment (sub compartment type) in which they were found; however, this relationship did not hold across different chromosomes.\n\nConclusionsThese analyses demonstrated that TEs are non-randomly distributed across many diverse genomes and were able to identify the specific TE superfamilies that were non-randomly distributed in each genome. Furthermore, going beyond the one-dimensional representation of the genome as a linear sequence was important to understand TE patterns within the genome. Additionally, we extended the utility of traditional community ecology methods in analyzing patterns of TE diversity.

genomics↗

bioRxiv2019

Variation in space and time: a long-term examination of density-dependent dispersal in a woodland rodent

Dispersal is a fundamental ecological process that can be affected by population density, yet studies report contrasting effects of density on propensity to disperse. Additionally, the relationship between dispersal and density is seldom examined using densities measured at different spatial scales or over extensive time-series. We used 51-years of trapping data to examine how dispersal by wild deer mice (Peromyscus maniculatus) was affected by changes in both local and regional population densities. We examined these patterns over both the entire time-series and also in ten-year shifting windows to determine whether the nature and strength of the relationship changed through time. Probability of dispersal decreased with increased local and regional population density, and the negative effect of local density on dispersal was more pronounced in years with low regional densities. Additionally, the strength of negative density-dependent dispersal changed through time, ranging from very strong in some decades to absent in other periods of the study. Finally, while females were less likely to disperse, female dispersal was more density-dependent than male dispersal. Our study shows that the relationship between density and dispersal is not temporally static and that investigations of density-dependent dispersal should consider both local and regional population densities.

ecology↗