Supporting code and data to reproduce analysis for: Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms

Seed dispersal affects gene flow and hence genetic differentiation of plant populations. During the Late Quaternary, most fruit-eating and seed-dispersing megafauna went extinct, but whether these animals have left signatures in the population genetics of their food plants, particularly those with large, ‘megafaunal’ fruits (i.e., > 4 cm – megafruits), remains unclear.

Here, we assessed the population history, genetic differentiation, and recent migration among populations of four animal-dispersed palm (Arecaceae) species with large (Borassus madagascariensis), medium-sized (Hyphaene coriacea, Bismarckia nobilis), and small (Chrysalidocarpus madagascariensis) fruits on Madagascar. We integrated double-digest restriction-site-associated DNA sequencing (ddRAD) of 167 individuals from 25 populations with (past) distribution ranges for extinct and extant seed-dispersing animals (e.g., giant lemurs, elephant birds), landscape and human impact data, and applied linear mixed-effects models to explore the drivers of genetic variation in Malagasy palms.

Palm populations that shared more megafrugivore species in the past had lower genetic differentiation than populations that shared fewer megafrugivore species. This suggests that megafrugivore-mediated seed dispersal in the past may have led to frequent gene flow among populations. In comparison, extant frugivore diversity only decreased genetic differentiation in the small-fruited palm. Furthermore, genetic differentiation decreased with landscape connectivity (i.e., environmental suitability, forest cover and river density), and human impact (i.e., road density) has decreased genetic differentiation among populations.

Synthesis: Our results suggest that the legacy of megafrugivores regularly achieving long dispersal distances is still reflected in the population genetics of palms that were formerly dispersed by such animals. Furthermore, low genetic differentiation was possibly maintained after the megafauna extinctions through alternative dispersal (e.g., human- or river-mediated), long generation times, and long lifespans of these megafruit palms. Our study illustrates how species interactions that happened >1000 years ago can leave imprints in population genetics.

Methods
We sampled leaf tissue from 25 natural populations of four palm species that differ in fruit sizes (large megafruits: B. madagascariensis; medium-sized megafruits: H. coriacea, B. nobilis; small fruits: C. madagascariensis) throughout their distribution in the western part of Madagascar during July, August and September of 2019 (Figure 1, Table 1, Table S1). More details on sampling for each species are provided in Table S1. The uneven number of sampled populations across the species mirrors the natural distribution and abundance of each species in Madagascar, with B. nobilis, H. coriacea and C. madagascariensis having wider distributions than B. madagascariensis. The latter is restricted and more fragmented in its distribution, and hence endangered according to the IUCN Red List of Threatened Species (IUCN, 2012).