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 ..., 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).
 , , # Data to reproduce analysis for: Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms

[https://doi.org/10.5061/dryad.pc866t1z6](https://doi.org/10.5061/dryad.pc866t1z6)

Authors: Méndez L., Barratt C. D., Durka W., Kissling W. D., Eiserhardt W. L., Baker W. J., Randrianasolo V., Onstein R. E.

**Contact**: Laura Méndez ([[e-mail]](mailto:[e-mail]))

## **Contents**

This data repository consists of the following folders and files:

Main folder (data_genomic_signatures_megafrugivore_dispersal_malagasy_palms):

·       Word document containing information on each file and instructions for use (**ReadMe.docx**)

·        “input” folder:

o   “BayesAss” folder:

§  Contains input files to run BayesAss (BA3-autotune.sh and BA3-SNPs.sh). Specifically, imputed modified .immanc files (by R script 03_modification_immanc_file.R) previously transformed to .immanc by PGDSpider and previously imputed by LinkImputeR (**Bm_modified.immanc, B...