ddRAD sequence data of palms (Arecaceae) of Madagascar

Seed dispersal is a key process in the generation and maintenance of genetic diversity and genetic differentiation of plant populations in tropical ecosystems. During the last 1000 years, Madagascar has lost all seed-dispersing megafauna (e.g., giant lemurs, elephant birds), but whether this has caused dispersal limitation, loss of genetic diversity, and increased genetic differentiation between plant populations with large, 'megafaunal' fruits (i.e., > 4 cm - megafruits) remains unclear. Here, we tested this hypothesis in four animal-dispersed Malagasy palm (Arecaceae) species with large megafruits (Borassus madagascariensis), medium-sized megafruits (Hyphaene coriacea, Bismarckia nobilis), and small fruits (Dypsis madagascariensis). We estimated species-level and population-level genetic diversity and genetic differentiation of 167 individuals from 25 populations, using double-digest restriction-site-associated DNA sequencing (ddRAD). To explore the drivers of genetic diversity and differentiation, we assembled (past) distribution ranges for extant and extinct seed-dispersing animal species, climate and human impact data. We detected relatively high genetic diversity in species with megafruits, with variation in population-level genetic diversity being explained by precipitation seasonality and absence of roads, rather than present or past frugivore richness. Genetic differentiation was lowest in species with medium-sized fruits, with population-level genetic differentiation decreasing among populations which shared more megafrugivore species in the past. These results contrast our prediction, and instead suggest that past dispersal events by megafauna may have increased gene flow between palm populations with megafruits, leading to high genetic diversity and low genetic differentiation, which has probably been maintained after the megafauna extinctions through human-mediated dispersal, long generation times, and long lifespans of these palms.