<i>k</i>-mer-based diversity scales with population size proxies more than nucleotide diversity in a meta-analysis of 98 plant species

A key prediction of neutral theory is that the level of genetic diversity in a population should scale with population size. However, as was noted by Richard Lewontin in 1974 and reaffirmed by later studies, the slope of the population size-diversity relationship in nature is much weaker than expected under neutral theory. We hypothesize that one contributor to this paradox is that current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads to a reference genome underestimate levels of genetic diversity in many species. As a first step to testing this idea, we calculated nucleotide diversity (π) and k-mer-based metrics of genetic diversity across 112 plant species, amounting to over 205 terabases of DNA sequencing data from 27,488 individuals. Methods The workflow we used to create these datasets is packaged as a snakemake workflow stored here: https://github.com/milesroberts-123/tajimasDacrossSpecies Please see the file named lewontin_paradox_methods_figures.pdf in the Zenodo submission attached to this repository for a full breakdown on the methods and references we used for SNP-calling, k-mer-counting, and scraping literature for genome size and life history variables. Some figures showing plots of the data in TableS2.xlsx are also included for reference.