Contemporary population genomic studies typically involve mapping raw reads to a reference genome and analyzing single nucleotide polymorphism (SNP) data obtained from variant calling. Despite the widespread use of the genotype caller GATK for variant calling, its design primarily for human data poses limitations in non-human species. Recently, ATLAS has emerged as a promising alternative caller, exhibiting superior performance with lower false positive and negative rates, significantly impacting phylogenomic inferences. However, the extent to which ATLAS versus GATK influences downstream population genomic analyses remains largely unexplored. To address this gap, we conducted a population genomic study on five Pterocarya species using GATK and ATLAS, alongside two reference genomes, P. stenoptera and P. macroptera. Analyzing four datasets, we evaluated mapping depth, coverage rate, linkage disequilibrium (LD), nucleotide diversity (π), population structure, and demographic history. Notably, using P. stenoptera as the reference genome resulted in less depth and coverage rate variation across species compared to P. macroptera. ATLAS consistently identified more SNPs, higher nucleotide diversity, and lower LD for both reference genomes. Population structure results were more sensitive to the choice of reference genome than callers, while both reference genomes and callers significantly influenced population demography inference. Our study emphasizes the critical impact of genotype caller and reference genome selection on downstream analyses. Based on current evidence, selecting a closely related reference genome and employing ATLAS for SNP calling are recommended to enhance the accuracy and reliability of population genomic studies.

Darwinian agriculture (also called Evolutionary agroecology) which focuses on the trade-off between individual fitness and community performance, can provide an efficient approach to enhance crop production. However, evolutionary or ecological processes, in particular the tragedy of the commons in crops, remain poorly understood. We used a pot experiment to examine whether wheat plants fell into this ‘tragedy’ when confronted with roots of an intra-variety neighbour and how the magnitude was influenced by soil fertility. Two varieties (old landrace Monkhead and modern variety 92-46) were selected for this study. Root competition scenarios were set by growing two plants of the same variety with a mesh or plastic partition. Soil fertility gradients were set by adding nutrient solutions with low or high application frequency. Biomass were tested and allometric relationship were analyzed to reveal resource allocation pattern. Old Monkhead had similar relative allocation to root biomass with modern 92-46, but had greater relative allocation to stem&leaf biomass and lower relative allocation to seed biomass. The presence of neighbour affected allometric relationships only in 4 out of 24 allometic comparisons, which all appeared in low fertility treatments. Fertilizer addition increased stem&leaf biomass allocation of Monkhead and decreased root and seed biomass allocation at the same time. By contrast, stem&leaf and seed allocation of 92-46 was not changed by fertilizer addition although root allocation was decreased. Our results demonstrated that there was a trade-off between non-reproductive and reproductive allocation for wheat varieties. There was not notable tragedy of the commons in wheat varieties, although a small degree was observed in Monkhead. Moreover, the occurrence and magnitude of the tragedy was dependent on resource availability and variety resource-use strategy. Our results underlie the importance of understanding the mechanisms behind the tragedy of the commons in crop varieties with different ecological strategies, and provide insights into the role of Darwinian agriculture in global food production.