Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

Summary
 

Research Aims - The extent of Madagascar’s grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C4 fire-adapted grass, Loudetia simplex, as a proxy for estimating grassland change through time. We carefully examined the utility of target-enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target-enrichment data and how assumptions about ploidy could affect analyses.
 

Methods - We developed a novel bioinformatic pipeline based to estimate ploidy and genotypes from target-enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data.
 

Key Result - All Malagasy Loudetia simplex individuals sampled in this study formed a clade a..., Methods are described in detail in Tiley et al. (2023).
Tiley GP, Crowl AA, Almary TOM, Luke WRQ, Solofondranohatra CL, Besnard G, Lehmann CER, Yoder AD, Vorontsova MS. 2023. Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar. bioRxiv. https://doi.org/10.1101/2023.04.07.536094, All software for analyses are discoverable through citations and publicly available. Input data and, where applicable, output files are provided for all empirical analyses.,