Comparing variation of innate immune genes between rodent species

Abstract

Emerging infectious diseases (EID) continue to threaten the persistence of wildlife populations. The standing genetic variation of a population can affect its ability to adapt to environmental changes like EID. Levels of variation at immune genes, such as toll-like receptor genes (TLR) of the innate immune system, are particularly relevant. The current study explores the role of demographic history in shaping the genetic variation of innate immune genes by comparing the standing genetic variation of five TLR genes and three nuclear autosomal control genes between two common native (bank vole (Myodes glareolus) and yellow-necked mouse (Apodemus flavicollis)) and one recently introduced rodent species (harvest mouse (Micromys minutus)). Samples from these species were collected in Southern Sweden, where all three species are sympatric. Results show significantly higher levels of overall genetic variation in the bank vole than the harvest mouse using both nucleotide diversity and haplotype diversity as measures of genetic variation. Specifically, bank vole nucleotide diversity is, on average and across all genes, 96% higher than that of the harvest mouse. When measured as haplotype diversity, genetic variation of bank voles is 68% higher than for harvest mice. The differences between bank voles and harvest mice are also significant when considering TLR genes only. Measures of nucleotide diversity show a significant difference between bank voles and yellow-necked mice. Across all genes, nucleotide diversity of bank voles is, on average, 83% higher than that of yellow-necked mice. No significant differences are found between the yellow-necked mouse and the harvest mouse. These findings demonstrate that the standing genetic variation of yellow-necked mice is closer to that of a recently bottlenecked population such as the harvest mouse, than the common bank vole. More generally these results suggest that bank voles have a higher adaptive potential to EID than both the yellow-necked mouse and the harvest mouse.

Popular Abstract

The rat race: immune genes and emerging infectious diseases

No better time than the present to talk about emerging infectious diseases. The Sars-CoV-2 virus shows us how detrimental a new pathogen can be for humans. Sadly, animals also face similar threats. As we know, wildlife is also pressured by other human-induced changes such as habitat loss, harvesting and much more. The scary thing is these disease outbreaks seem to be increasing.

In most cases, higher levels of genetic variation in a population mean it has a greater potential to adapt to changes, like new diseases. For diseases, the genetic variation of immune genes is especially relevant. Immune genes include innate immune genes, that shape an organism’s first line of defence. By comparing the genetic variation of innate immune genes between various species, we can learn more about differences in their ability to adapt to new diseases, and the drivers of these differences.

Rodents make great study organisms for these kinds of studies. This is because rodents are both important components of our ecosystems and potential disease reservoirs for human populations. In Southern Sweden, bank voles (Myodes glareolus) and yellow-necked mice (Apodemus flavicollis) are commonly found in the wild. In contrast, the harvest mouse (Micromys minutus) arrived from Denmark in the 1990s when it presumably went through a drastic bottleneck which should have reduced genetic variation. By comparing the genetic variation of innate immune genes between these species, we can see what the impacts of demographic events are on this variation. This is exactly what we did in my project. Specifically, we focused on genes of the innate immune system known as toll-like receptor genes.

How did we do this?
It all started with some field work in the Revingehed area, 20km east of Lund. Here we did live trapping to get skin samples. Back in the lab we extracted DNA from the samples and sequenced it. Statistical tests were then done to quantify genetic variation.

So, what did we find?
Given the bank vole and the yellow-necked mouse are both common and abundant species in Southern Sweden, we expected them to have similar levels genetic variation. What we found was that, in this sense, the yellow-necked mouse is closer to the harvest mouse, and bank voles have the highest levels of genetic variation. This suggests bank voles could better adapt to emerging infectious diseases than yellow-necked mice. Though we did expect the small harvest mouse coloniser population to have low levels of genetic variation, we didn’t think the yellow-necked mouse would too. One way to explain this is by looking back in time a little, around 20 000 years ago. Back then, bank voles and yellow-necked mice were recolonizing Fennoscandia after the last ice age. They did this in very different ways, which could explain the patterns we observed.

Master’s Degree Project in Biology, credits: 45
Department of Biology, Lund University

Advisor: Lars Råberg
Functional Zoology

• author: Dwivedi, Nisha
• supervisor: Lars Råberg
• organization: Degree Projects in Biology
• course: BION02 20202
• year: 2021
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 9057841
• date added to LUP: 2021-06-22 15:50:59
• date last changed: 2021-06-22 15:50:59