Genomic signatures of past megafrugivore‐mediated dispersal in Malagasy palms

Abstract

Abstract 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 (e.g., giant lemurs and elephant birds) and extant seed‐dispersing animals, 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 of all palm species decreased with landscape connectivity (i.e. environmental suitability, forest cover and river density) and human impact (i.e. road density), while migration rates of the small‐fruit palm increased with road density. 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 their population genetics.