Jasper, M. E. | Search bioRxiv

bioRxiv2021

Estimating dispersal using close kin dyads: The KINDISPERSE R package

Investigating dispersal in animal populations can be difficult, particularly for taxa that are hard to directly observe such as those that are small or rare. A promising solution may come from new approaches that use genome-wide sequence data to detect close kin dyads and estimate dispersal parameters from the distribution of these dyads. These methods have so far only been applied to mosquito populations. However, they should have broad applicability to a range of taxa, although no assessment has yet been made on their performance under different dispersal conditions and study designs. Here we develop an R package and Shiny app, O_SCPLOWKINDISPERSEC_SCPLOW, that can be used to estimate dispersal parameters from the spatial distribution of close kin. KO_SCPLOWINDISPERSEC_SCPLOW can handle study designs that target different life stages and allows for a range of dispersal kernel shapes and organismal life histories; we provide implementation examples for a vertebrate (Antechinus) and an invertebrate (Aedes). We use simulations run in O_SCPLOWKINDISPERSEC_SCPLOW to compare the performance of two published close kin methodologies, showing that one method produces unbiased estimates whereas the other produces downward-biased estimates. We also use O_SCPLOWKINDISPERSEC_SCPLOW simulations to investigate how study design affects dispersal estimates, and we provide guidelines for the size and shape of sample sites as well as the number of close kin needed for accurate estimates. O_SCPLOWKINDISPERSEC_SCPLOW is easily adaptable for application to a variety of research contexts ranging from invasive pests to threatened species where non-invasive DNA sampling can be used to detect close kin.

genetics↗

bioRxiv2019

A LAMP assay for the rapid and robust assessment of Wolbachia infection in Aedes aegypti under field and laboratory conditions

With Wolbachia-based arbovirus control programs being scaled and operationalised around the world, cost effective and reliable detection of Wolbachia in field samples and laboratory stocks is essential for quality control. Here we validate a modified loop-mediated isothermal amplification (LAMP) assay for routine scoring of Wolbachia in mosquitoes from laboratory cultures and the field, applicable to any setting. We show that this assay is a rapid and robust method for highly sensitive and specific detection of wAlbB Wolbachia infection within Aedes aegypti under a variety of conditions. We test the quantitative nature of the assay by evaluating pooled mixtures of Wolbachia-infected and uninfected mosquitoes and show that it is capable of estimating infection frequencies, potentially circumventing the need to perform large-scale individual analysis for wAlbB infection status in the course of field monitoring. These results indicate that LAMP assays are useful for routine screening particularly under field conditions away from laboratory facilities.\n\nImportanceReleases of mosquitoes infected with strains of Wolbachia bacteria are expanding around the world because this bacterium that lives inside cells provides an effective tool to suppress mosquito populations and the ability of mosquitoes to transmit viruses. The success of the release programs relies on rapid and effective means of detecting Wolbachia and scoring their frequencies in mosquitoes for quality control and for assessing the success of releases. Here we test a \"LAMP\" (Loop-mediated isothermal amplification) assay for robust detection of Wolbachia infections in laboratory and field mosquito populations. We show that the assay can detect the bacteria when present at a low density in samples, and with a high degree of reproducibility. The assay uses a simple protocol which requires minimal training. It can readily detect Wolbachia in mosquitoes obtained from traps that are routinely used in field surveys. The assay should be cost effective in a variety of settings.

genetics↗