Genomic demography predicts community dynamics in a temperate Montane forest
Data files
Jun 17, 2025 version files 60.68 MB
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README.md
3.37 KB
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WFDP_SNPS.zip
60.68 MB
Abstract
Species population sizes fluctuate over time, and these temporal dynamics play a key role in maintaining biodiversity. While multiple modeling approaches have been developed to characterize fluctuations in forest tree species abundances, the data required to parametrize these models from scratch are substantial. Here we introduce a novel approach to modeling population fluctuations on decadal timescales by relating community-level dynamics to population-level patterns encoded in plant genomes. Using a single genomic snapshot to generate contemporary effective population size estimates in a temperate montane forest, we accurately predict fluctuations across three censuses. Our approach opens the door for the use of genomic demography to parametrize multispecies community models in ecology and shows that population genomic data can provide accurate predictions for ecological dynamics.
Dataset DOI: 10.5061/dryad.9w0vt4bsx
Description of the data and file structure
SNPs in VCF format for 8 species of trees from the Wind River Forest Dynamics plot in Southwestern Washington, USA.
Files and variables
File: WFDP_SNPS.zip
Description: We have submitted the population SNPs.vcf (Variant Call Format) file from the de novo assembly performed using the STACK software.
This file is the primary dataset utilized for the various analyses described in our article, "Genomic Demography Predicts Community Dynamics in a Temperate Montane Forest."
The article investigates the application of genetic estimates of effective population size to predict population fluctuations given a community mean field model.
Description of the data and file structure
Dataset Overview
This Variant Call Format (VCF) file contains Single Nucleotide Polymorphism (SNP) data from 8 species of trees with varying numbers of individuals. Species names and codes are depicted below, along with the number of individuals per species and the number of SNP loci per species. VCF files are named according to the species code.
| Species | Code | N | Loci |
|---|---|---|---|
| Thuja plicata | THPL | 93 | 55386 |
| Tsuga heterophylla | TSHE | 92 | 8777 |
| Cornus nuttalli | CONU | 90 | 6502 |
| Acer circinatum | ACCI | 92 | 588 |
| Pseudotsuga menziesii | PSME | 92 | 9373 |
| Taxus brevifolia | TABR | 93 | 8892 |
| Abies amabilis | ABAM | 94 | 24279 |
| Abies grandifolia | ABGR | 48 | 7875 |
populations.snps.vcf
File Details
* File Name: CODE.vcf
* File Format: VCF (Variant Call Format)
* Date: 5/28/2025
* Source Software: Stacks v2.41
Data Description
The VCF file includes the following columns standard to the format:
* #CHROM: Chromosome number
* POS: Position of the SNP on the chromosome
* ID: Identifier of the SNP
* REF: Reference base
* ALT: Alternate base(s)
* QUAL: Quality score of the SNP
* FILTER: Filter status
* INFO: Additional information (e.g., allele frequency, number of samples)
* FORMAT: Data format
* Sample columns: One per individual, containing genotype information
Specific Fields in INFO
* NS: Number of samples with data
* AF: Allele frequency
* DP: Total depth of reads
Specific Fields in FORMAT
* GT: Genotype
* AD: Allele depth
* DP: Read depth
* GQ: Genotype quality
* GL: Genotype likelihood
Code/software
The VCF file can be opened and analyzed using various bioinformatics tools and software. Some of the most common include:
* IGV (Integrative Genomics Viewer): Useful for visualizing genomic data.
* BCFtools: Command-line tool for working with VCF/BCF files, including filtering, viewing, and converting.
* GATK (Genome Analysis Toolkit): Provides tools to analyze high-throughput sequencing data with a focus on variant discovery.
* vcftools: Command-line program designed to work specifically with VCF files to perform various types of analyses.