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.

种子传播（seed dispersal）会影响基因流，进而作用于植物种群的遗传分化。在晚更新世时期，多数以果实为食、参与种子传播的巨型动物群（megafauna）走向灭绝，但这些动物是否会在其取食植物的种群遗传学中留下印记，尤其是那些具有大型“巨型果实”（即直径＞4cm的巨型果实）的植物，目前仍不明确。
本研究针对马达加斯加岛上4种由动物传播种子的棕榈科（Arecaceae）植物展开种群历史、遗传分化与近期迁移模式的评估，这4个物种分别结有大型果实（Borassus madagascariensis）、中等大小果实（Hyphaene coriacea、Bismarckia nobilis）以及小型果实（Chrysalidocarpus madagascariensis）。我们整合了来自25个种群共167个个体的双酶切限制性位点相关DNA测序（double-digest restriction-site-associated DNA sequencing，ddRAD）数据，结合已灭绝与现存种子传播动物（如巨狐猴、象鸟）的历史分布范围、景观与人类活动影响数据，并运用线性混合效应模型探究马达加斯加棕榈种群遗传变异的驱动因素。
研究发现，历史上共享更多巨型食果动物物种的棕榈种群，其遗传分化程度低于共享此类动物较少的种群。这表明过去由巨型食果动物介导的种子传播，可能促成了种群间频繁的基因流。相较而言，现存食果动物的多样性仅能降低小型果实棕榈的遗传分化。
此外，种群遗传分化程度随景观连通性（即环境适宜性、森林覆盖率与河流密度）升高而降低，而人类活动影响（即道路密度）同样降低了种群间的遗传分化。
综合分析结果显示，曾由这类巨型食果动物完成长距离种子传播的棕榈物种，其种群遗传学特征仍保留着巨型食果动物历史生态作用的印记。此外，在巨型动物群灭绝后，这类巨型果实棕榈可能通过替代传播途径（如人类或河流介导的传播）、较长的世代时长与寿命维持了较低的遗传分化水平。
本研究阐明了距今逾千年的物种互作如何在种群遗传学中留下印记。