DOI: 10.5061/dryad.905qfttqx
title: Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

description: 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 and possibly indicated an ancestral
 high-altitude distribution. Demographic models suggested grassland
 expansions occurred prior to the Last Interglacial Period and supported
 extensive grasslands prior to human colonization. Though there are
 limitations to target-enrichment data for population genetic studies, we
 find that analyses of population structure are reliable.   Key
 Point - Genetic variation in Loudetia simplex supports widespread
 grasslands in Madagascar prior to the more recent periods of notable
 paleoclimatic change. However, the methods explored here could not
 differentiate between paleoclimatic change near the Last Glacial Maximum
 and anthropogenic effects. Target-enrichment data can be a valuable tool
 for analyses of population structure in the absence a reference genome.
   Societal Impact Statement   Recognizing Loudetia
 dominated grasslands were widespread prior to human colonization
 highlights that open ecosystems were and continue to be an important
 component to Madagascar’s biodiversity. Urgently required are biodiversity
 inventories and risk assessments for unique grassland flora and fauna
 under present day environmental conditions to recognize and quantify
 modern human impacts within ecosystems historically regarded as
 wastelands. Substantial financial and logistic barriers exist to
 implementing conservation studies using contemporary genomic tools that we
 seek to ameliorate by developing computational resources to leverage a
 cost-effective data generation strategy that requires no prior genetic
 knowledge of the target species.
description: 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
description: All software for analyses are discoverable through citations and
 publicly available. Input data and, where applicable, output files are
 provided for all empirical analyses.