Effects of harvesting and stubble management on abundance of pest rodents (Mus musculus) in a conservation agriculture system

BACKGROUND: The shift to more environmentally sensitive agricultural practices over the last several decades has changed farmland landscapes worldwide. Changes including no-till and retaining high biomass mulch has been coincident with an increase in rodent pests in South Africa, India, South America and Europe, indicating a possible conflict between conservation agriculture (CA) and rodent pest management. Research on effects of various crop management practices associated with CA on pest rodent population dynamics is needed to anticipate and develop CA-relevant management strategies. RESULTS: During the Australian 2020–2021 mouse plague, farmers used postharvest stubble management practices, including flattening and/or cutting, to reduce stubble cover in paddocks to lessen habitat suitability for pest house mice. We used this opportunity to assess the effects of both harvest and stubble management on the movement and abundance of mice in paddocks using mouse trapping and radio tracking. We found that most tracked mice remained resident in paddocks throughout harvest, and that mouse population abundance was generally unaffected by stubble management. CONCLUSION: Recent conversions to CA practices have changed how pest house mice use cropped land. Management practices that reduce postharvest habitat complexity do not appear to reduce the attractiveness of paddocks to mice, and further research into new management strategies in addition to toxic bait use is required as part of an integrated pest management approach.</p

Comparison of SNP genotypes generated by GigaMUGA genotyping and custom hybridization capture sequencing applied to the same subset of samples.

Comparison of SNP genotypes generated by GigaMUGA genotyping and custom hybridization capture sequencing applied to the same subset of samples.</p

Sampling locations of house mice trapped for SNP genotyping (2019–2020).

Sampling locations of house mice trapped for SNP genotyping (2019–2020).</p

Estimated genotyping cost comparison between array genotyping and custom hybridization capture sequencing panel.

Estimated genotyping cost comparison between array genotyping and custom hybridization capture sequencing panel.</p

Analysis of population genetic variation based on filtered GigaMUGA genotypes (49,058 SNPs) from 70 mice sampled at five locations in southeastern Australia.

(A) Results of PCA, with axes representing the first two principal components along with percentage of total genetic variation explained. Points are individual samples with inertia ellipses shown for each population. (B) Results of DAPC, which identifies synthetic variables that maximize the differences among populations. LD1 and LD2 are the first two linear discriminants, along with respective percentage of interpopulation variation explained. Population means are connected by dashed lines representing the minimum spanning tree based on the squared distances among populations.</p

Target SNP sequencing coverage from hybridization sequence capture.

Each curve represents a different sample (N = 317), and the observed proportion of targeted SNPs (3,651 total) that had coverage equal to or greater than the value indicated on the x-axis.</p

Comparison of pairwise kinship values, estimated using PC-Relate for the same samples (N = 47) using both the GigaMUGA genotyping (x-axis) and custom hybridization capture sequencing SNP datasets (y-axis).

Each point represents a unique dyad, colored by the corresponding degree of kinship.</p

Details of custom hybridization capture sequencing panel for genotyping house mice in southeastern Australia cropping regions.

Details of custom hybridization capture sequencing panel for genotyping house mice in southeastern Australia cropping regions.</p

Characterization of population genetic variation based on hybridization capture sequencing dataset for house mice (N = 317) sampled from two adjoining farms in Adelaide Plains, SA (AP1 and AP2).

(A) PCA, with samples plotted against first (x-axis) and second (y-axis) principal components (PCs). Percentage of total genetic variation explained by each axis provided in parentheses. (B) Density plot for individual samples (ticks on x-axis) along linear discriminant (LD) function from DAPC (25 PCs, 1 LD). (C) Posterior membership probabilities (colors) for individual mice (columns) to each population, with sampling location indicated by arrows at top of plot.</p

Distribution of distances (in bp) between 10,722 non-targeted SNPs and the nearest targeted SNP in sequence capture dataset.

Distribution of distances (in bp) between 10,722 non-targeted SNPs and the nearest targeted SNP in sequence capture dataset.</p