DOI: 10.5061/dryad.9w0vt4bsx
title: Genomic demography predicts community dynamics in a temperate Montane forest

description: 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.
description: # Genomic demography predicts community dynamics in a temperate Montane
 forest Dataset DOI: [10.5061/dryad.9w0vt4bsx](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.