Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms

Abstract

Background: Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear. We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used 16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms.

Results: Using GBS we identified 18,000 SNPs across 400 individuals sampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time.

Conclusion: We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next-generation sequencing (NGS) techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.

Keywords: Genotyping-by-sequencing; Housefly; Isolation by distance; Microbiome; Musca domestica; Pathogens; Population structure; SNPs; Vector.

Fig. 1

Principal coordinates analysis of SNPs. Plots of the values of the first two components for males collected in early summer (a), females collected in early summer (b), males collected in late summer (c), and females collected in late summer (d). Numbers indicate the farms from which individual flies were collected and numbered as in Table 1

Fig. 2

Least square regression of the geographic distance versus the genetic distance (Mantel test) of males collected in early summer (a) (slope: 5.70E-05, R² = 0.51, p < 0.0001), females collected in early summer (b) (slope: 7.82E-05, R² = 0.60, p < 0.0001), males collected in late summer (c) (slope: 4.81E-05, R² = 0.71, p < 0.0001), and females collected in late summer (d) (slope: 6.14E-05, R² = 0.65, p < 0.0001)

Fig. 3

Beta diversity of 11 housefly populations. Non-metric multi-dimensional scaling analysis of houseflies collected in early summer (a), late summer (b), females (c), and males (d). Samples are colored by population, and those representing the same population are surrounded by a polygon

Fig. 4

Hierarchially clustered heatmap of relative potential pathogen prevalence. Organisms were selected using a short list of potential pathogenic organisms associated with houseflies. Only organisms that were observed as 0.1% or more of total reads in more than one sample were included. The samples and species were clustered using Bray-Curtis distances, and the sample dendrogram is colored by collection time

Fig. 5

Map of the zone of collections. Sample locations are designated with a number. In total flies from 11 locations (dairy farms) were sampled throughout Denmark. A GeoDanmark Basis map was downloaded from the Danish “Geodatastyrelsen”, October 2016, Styrelsen for Dataforsyning og Effektivisering. The figure is similar, but not identical to the original image, and is therefore for illustrative purposes only