The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species

Abstract

Demographic factors are intrinsically crucial to evaluate species extinction risk. However, measuring them remains difficult and time-consuming and the use of genomic summary statistics has been advocated to assess the conservation status of a species. In the present study, we estimated (i) the census number (Nc), (ii) effective population size (Ne) over three different time periods, recent, historical and ancient, (iii) neutral genetic diversity ({pi}4), and (iv) a measure of the efficacy of purifying selection ({pi}0/{pi}4) for 101 plant species using population genomic sequencing data. Twenty-one species are from the Plant Species with Extremely Small Populations (PSESP) program of SW China. Threatened species exhibited significantly lower Ne, Nc,{pi} 4, and weaker purifying selection, but had a higher Ne/Nc ratio than non-threatened ones. Nc was the main determinant in identifying conservation status, and contemporary neutral genetic diversity was predominantly influenced by historical Ne. In the absence of demographic information, genetic parameters are a good proxy of conservation status, likely because currently threatened species also had a low historical population size. In summary, our findings suggest that direct estimates of Nc are more useful than{pi} 4, although the latter remains a valuable conservation indicator. Hence, efforts such as the PSESP should be extended. Significance StatementExtinction is essentially a demographic process. However, evaluating the risk of extinction of species based only on demographic parameters remains a difficult task, and today only 18% of plant species are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Here, we use demographic data and whole genomic data from 101 plant species to show that while census number remains the best predictor of extinction risk, genomic based parameters provide good alternatives. More specifically, current neutral nucleotide diversity and historical effective population size are good predictors of the extinction risk of plant species.