Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island

Abstract

Summary Past climatic fluctuations have played a major role in shaping the current plant biodiversity. Although harbouring an exceptional biota, oceanic islands have received little attention in studies on species demographic history and past vegetation patterns. We investigated the impact of past climatic changes on the effective population size of a tree (Coffea mauritiana) that is endemic to Reunion Island, located in the south‐western Indian Ocean (SWIO). Demographic changes were inferred using summary statistics calculated from genomic data. Using ecological niche modelling and the current distribution of genetic diversity, the paleodistribution of the species was also assessed. A reduction in the effective population size of C. mauritiana during the last glaciation maximum was inferred. The distribution of the species was reduced on the western side of the island, due to low rainfall. It appeared that a major reduction in rainfall and a slight temperature decrease prevailed in the SWIO. Our findings indicated that analyses on the current patterns of intraspecific genetic variations can efficiently contribute to past climatic changes characterisation in remote islands. Identifying area with higher resilience in oceanic islands could provide guidance in forest management and conservation faced to the global climate change.

Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

“…The stairway plot also suggested that R. cyanocarpum underwent a population expansion in the period before and after the Last Glacial Maximum (LGM, 0.04–0.006 Ma) ( Garot et al, 2019 ). That this population expansion event took place was also supported by the negative value of Tajima’s D (–0.2748 with 95% confidence level), because strong negative values of Tajima’s D can indicate population expansions ( Tajima, 1989a ).…”

Multi-Approach Analysis Reveals Local Adaptation in a Widespread Forest Tree of Reunion Island

“…Raw data were retrieved from the European Nucleotide Archive no PRJEB31715 ( Garot et al 2019b ). Briefly, leaves at the same developmental stage (third leaf from the end of the plagiotropic branch) were sampled in the collection, using the same sampling design as for phenotypic measurements ( Supplementary Table S6 , Fig.�6 ), and were immediately frozen in liquid nitrogen.…”

“…Frozen leaves were then stored at −80�C until RNA extraction. Total RNA extraction, cDNA library construction and single-end sequencing using HiSeq 2500 (Illumina, 100 nt) were performed as described in Garot et al (2019b ). Due to technical difficulties encountered when extracting RNA from a sample, sequencing data were only available for 23 of the 24 accessions.…”

“…SNP calling was performed according to Garot et al (2019b ) using the Genome Analysis Toolkit pipeline ( De Pristo et al 2011 ). The following filters were applied to the SNP dataset: SNPs with <10 reads (DP < 10) per individual and Genotype Quality <30 (GQ < 30) per individual were filtered out using BCFtools v.1.3 in the SAMtools package; all SNPs with missing values (not available, NAs), low allelic frequencies (minor allele frequency, MAF < 0.06) and that applied to only one population were removed using VCFtools v. 0.1.13 ( Danecek et al 2011 ).…”

“…According to genetic studies, C. mauritiana individuals mainly cluster according to the site of plant sampling (source populations), with further grouping in genetic clusters showing regional distribution ( Garot et al 2019a ). During the Last Glaciation Maximum, the size of C. mauritiana population was reduced ( Garot et al 2019b ) and the distribution of this species was likely restricted to the rainy windward side of the island. The current species distribution appears to be associated with a recent expansion of the species across the island ( Garot et al 2019b ) and includes both gradients of temperature (13–24�C in mean annual temperature) and rainfall (from 1,100 to up to 5,000 mm in median annual precipitation) ( Supplementary Fig.…”