DOI: 10.5061/dryad.qjq2bvqm0
title: Retracing the center of origin and evolutionary history of nutmeg <em>Myristica fragrans</em>, an emblematic spice tree species

description: The study of plant origins, since Nikolaï Vavilov's foundational
 work, emphasizes the importance of identifying centers of origin for
 cultivated species, which exhibit high genetic diversity in their native
 areas, impacting conservation and sustainable management. This research
 seeks to determine the origin and evolutionary history of nutmeg
 (Myristica fragrans; Myristicaceae), traditionally believed to originate
 from Indonesia's Banda Islands in the Southern Moluccas. We explored
 nutmeg's genetic diversity across the Moluccas archipelago using
 nuclear microsatellite markers and whole plastid genome sequences. Our
 results identified two primary genetic clusters: one in the North Moluccas
 (Ternate, Tidore, and Bacan islands) with higher diversity, and another in
 the South Moluccas (Banda and Ambon islands), which exhibited signs of a
 recent bottleneck. Through Approximate Bayesian Computation (ABC)
 analyses, we inferred that nutmeg migrated from South to North Moluccas
 during the late Pleistocene to early Holocene, confirming the South
 Moluccas as its center of origin. These findings suggest a
 naturally-driven distribution influenced by migration and past climate
 changes. Human activities have further shaped these patterns, providing
 essential insights for developing targeted conservation strategies for
 nutmeg based on its genetic diversity.
description: # Retracing the center of origin and evolutionary history of nutmeg
 *Myristica fragrans*, an emblematic spice tree species Dataset DOI:
 [10.5061/dryad.qjq2bvqm0](10.5061/dryad.qjq2bvqm0) ## Description of the
 data and file structure **DNA sequence analysis** We provide the scripts
 used to prepare, quality-check, filter, map, align, and call SNPs from the
 whole-genome chloroplast sequencing dataset of nutmeg. All scripts for
 cleaning, mapping, and SNP calling are included in
 **Supplementary_File_2.txt**. While the Supplementary_File_2.pl is to
 filter the FASTQs on mean quality. The corresponding launch scripts for
 each step are also provided as **Prepare.sh**, **Mapping.sh**, and
 **Calling.sh**. Supplementary_File_2.txt Supplementary_File_2.pl
 Calling.sh Prepare.sh Mapping.sh Once the *.vcf *files are generated using
 the **Calling.sh** script, they can be converted into FASTA and NEXUS
 formats for subsequent DIYABC analysis and haplotype network construction.
 Please use PopArt ver 1.7 for Mac OSx to generate the haplotype network.
 **Naming the file** We used the file *Moluccas.txt* to assign names to
 each sequence. This file lists all sample names (only names) included in
 the cpDNA analysis. Moluccas.txt **Fst** Here, we estimated F~ST~ using
 the microsatellite dataset. The analysis was performed in R with the
 *hierfstat* package, using a Genepop-formatted file. The file used
 (*DIYABC_-_Fragmented_both_reduced.txt*) is a converted version of the
 original *.mss* dataset to ensure compatibility with the software. Please
 use the following file as an input: DIYABC_-_Fragmented_both_reduced.txt
 We will use the following script using R ver 3.6 to analyze them. We used
 package of *hierfstat* ver 0.5 to analyze the F~ST~ : Fst.txt **DIYABC**
 Complete dataset for DIYABC analysis and population genetics. Please use
 the non-interface version of DIYABC ver 2.1. Use the following files as
 prerequisites for generating priors in DIYABC: * reftableRF.bin *
 statobsRF.txt * headerRF.txt These files can be created directly through
 the DIYABC interface or manually, provided you follow the same file format
 requirements. The file `reftableRF.bin` contains a simulated reference
 table generated by the DIYABC Random Forest software. This file stores the
 simulated datasets produced after defining the demographic prior
 parameters in DIYABC (e.g., divergence time, mutation rate, effective
 population size, and historical scenarios). This file cannot be opened or
 read directly as a text or table file, because it is a binary file
 specific to DIYABC Random Forest. It can only be accessed and interpreted
 through the DIYABC Random Forest interface or workflow. To reproduce or
 regenerate this file, users must: 1. Install the DIYABC Random Forest
 software. 2. Define the demographic and historical prior parameters within
 the software (e.g., time, mutation rate, population size, migration
 parameters). 3. Run the simulation procedure in DIYABC Random Forest to
 generate a new `reftableRF.bin` file. No other software can be used to
 open or visualize this file directly. Therefore, access to this file is
 restricted to the DIYABC Random Forest environment and its associated
 analysis pipeline. The file *headerRF.txt* provides the prior information
 for each demographic parameter, and *statobsRF.txt* contains the summary
 statistics for the observed data. Use the Genepop data format to analyze
 population divergence. In this study, we used three files: *
 *DIYABC_-_Fragmented_both_reduced.mss* (combined SSR + cpDNA data), *
 *DIYABC_-_Fragmented_cpDNA.mss* (cpDNA data only), *
 *DIYABC_-_Fragmented_SSR.mss* (SSR data only). Each *.mss* file is a
 simple plain-text format that can be directly read by DIYABC. You may use
 R or any text editor to convert or inspect these files. *
 DIYABC_-_Fragmented_both_reduced.mss * DIYABC_-_Fragmented_cpDNA.mss *
 DIYABC_-_Fragmented_SSR.mss To launch the DIYABC analysis, please use this
 script and adjust the parameters as per your research, then you can launch
 your own analysis in your HPC environment. ABC_world.sh You will generate
 the priors, and if you're ok with your priors, then you can go and
 launch the demographic analysis, such as time and population size.