DOI: 10.5061/dryad.d51c5b05s
title: Rapid diversification of gray mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula

description: Biological systems occurring in ecologically heterogeneous and spatially
 discontinuous habitats provide an ideal opportunity to investigate the
 relative roles of neutral and selective factors in driving lineage
 diversification. The gray mangroves (Avicennia marina) of Arabia occur at
 the northern edge of the species’ range and are subject to variable, often
 extreme, environmental conditions, as well as to historic large
 fluctuations in habitat availability and connectivity resulting from
 Quaternary glacial cycles. Here, we analyze fully sequenced genomes
 sampled from 20 locations across the Red Sea, the Arabian Sea, and the
 Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the
 species in the region and to identify adaptive mechanisms of lineage
 diversification. Population structure and phylogenetic analyses revealed
 marked genetic structure and highly supported clades among and within the
 seas surrounding the Arabian Peninsula. Demographic modeling showed times
 of divergence consistent with recent periods of geographic isolation and
 low marine connectivity during glaciations, revealing the presence of
 (cryptic) glacial refugia in the Red Sea and the PAG. Significant
 migration was detected within the Red Sea and the PAG, and across the
 Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary
 contact among Arabian mangrove populations. Genetic‐environment
 association analyses revealed high levels of adaptive divergence and
 detected signs of multi-loci local adaptation driven by temperature
 extremes and hypersalinity. These results support a process of rapid
 diversification resulting from the combined effects of historical factors
 and ecological selection and reveal mangrove peripheral environments as
 relevant drivers of lineage diversity.
description: Details in the corresponding mansucript and the README file.
description: # Datasets and Supplementary Materials for the article: “Rapid
 diversification of gray mangroves (Avicennia marina) driven by geographic
 isolation and extreme environmental conditions in the Arabian Peninsula”
 Deposited in DRYAD DOI: 10.5061/dryad.d51c5b05s Here we report all the
 necessary datasets to reproduce the phylogenomics, population genomics,
 demographic and genotype-environment association analyses carried out in
 the article ‘Rapid diversification of gray mangroves (Avicennia marina)
 driven by geographic isolation and extreme environmental conditions in the
 Arabian Peninsula’, published in Molecular Ecology. For details on data
 generation please refer to the article. Article DOI:10.1111/mec.17260 Last
 updated: January 4, 2024 ## Description of the data and file structure:
 The data is structured in two subdirectories. 1. RDA_Datasets: Data files
 used in genotype-environment association studies with redundancy analysis:
 * MangSamples170_coords.txt: Population and geographic coordinates for
 each mangrove individual. * Mang_ClimCoords.txt: georeferenced
 environmental data for each sample analyzed in the article. *
 GEA_EcologicalVariables: Description of Ecological variables present in
 the file 'Mang_ClimCoords.txt' * 012 and indv files: Alternative
 allele count files and sample lists used in the RDA. *
 GOdatabase_32CHROM.txt: Annotated list of genes and genomic coordinates
 for candidate gene identification (check or genome report for more details
 on the reference and annotation):
 *
 Empty cells indicates missing values. 2.fastsimcoal: Site frequency
 spectra, .est and .tpl input files for the eight demographic models tested
 with fastsimcoal2. ## Sharing/Access information: Resequencing raw data is
 deposited in the SRA database, accession BioProject: PRJNA629068. NCBI
 biosample accession numbers are provided in Table S1 of the article
 (Supporting Information). ## Code/Software: R script for redundancy
 analysis (RDA) conducted in the article: The R script is provided
 separately as related software. R analyses were carried out in RStudio v
 1.1.463 (R Studio Team, 2015) with R v3.5.3 (R Core Team, 2019). *Used
 Packages: sdmpredictors sp raster maptools rgdal rJava psych caret RPMG
 factoextra curl vroom pcadapt qvalue vegan qqman robust gdata fields