Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda.

Rémi Tournebize,Valérie Poncet,Alexandre De Kochko,Yves Vigouroux,François Munoz,Stéphanie Manel

doi:10.1371/journal.pone.0183412

Abstract

Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion.

Highlights

Climatic fluctuations have prevailed throughout the Quaternary period, influencing species distribution and population dynamics through an alternation of expansion, contraction and fragmentation phases [1, 2]
Genetic structure analyses based on whole-genome resequencing dataset (100k single nucleotide polymorphisms (SNPs)) supported a phylogeographic pattern consisting in two main (K = 2) latitudinally distinct groups, denoted as “North” and “South” groups (S1 Fig)
We found that an early population of Amborella could have split into two distinct Pleistocene ancestral populations about 23,400 years BP, one in the North and another in the South

Summary

Introduction

Climatic fluctuations have prevailed throughout the Quaternary period, influencing species distribution and population dynamics through an alternation of expansion, contraction and fragmentation phases [1, 2]. These dynamics have shaped the current distribution and structuring of intra-specific genetic diversity [3]. Modelling species’ demographic history from present patterns of genetic diversity should allow identifying the influence of these past dynamics [5, 6]. Demo-genetic models allow inferring the plausible past demographic and migration dynamics that shaped the distribution of neutral genetic polymorphisms observed in current populations [7]. The inferred variations in effective population size Ne can reveal the imprint of fluctuating climatic conditions on species’ demographic and range dynamics [8]

Objectives

Methods

Results

Conclusion