Is genomic diversity a useful proxy for census population size? Evidence from a species-rich community of desert lizards

Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long-term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome-wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long-term estimates of abundance, occupancy, and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to ask whether ecological preference exerts a measurable effect on geneti...