DOI: 10.5061/dryad.9ghx3ffqw
title: Data from: Spatial genetic structure of two conifers in a highly human-modified landscape of central Mexico

description: Forests have been globally reduced by unprecedented rates of deforestation
 and habitat transformation, which can affect the species’ genetic
 structure. Understanding patterns of spatial genetic structure is
 fundamental for proposing conservation actions that contribute to their
 long-term persistence. This study evaluated the spatial genetic structure
 and the effects of landscape features on gene flow in two conifers, Abies
 religiosa and Pinus montezumae, with different successional affinities in
 the temperate forest of La Malinche National Park (LMNP) in central
 Mexico, which exhibits a complex topography and high land-use changes. We
 recovered 7,326 single-nucleotide polymorphisms (SNPs) for A. religiosa
 and 34,423 for P. montezumae across 12 sites in four mountain slopes.
 Clustering analyses did not reveal genetic structure in both species, and
 Moran Eigenvector Maps showed that only 3% of the genetic variation was
 spatially structured in A. religiosa, whereas in P. montezumae the model
 did not fit the data (R2 = -0.01). A weak isolation by distance pattern
 was found only for A. religiosa (r = 0.12, P &lt; 0.05), and in P.
 montezumae, 11% of the genetic variation was structured among slopes.
 Landscape genetic analyses showed that topography, aspect, and land use
 did not explain genetic differentiation more than a null model of
 geographic distance in A. religiosa, in contrast to P. montezumae, in
 which the aspect-sine surface was the top-ranked model, indicating a
 reduction of gene flow Eastward. Our study contributes information for the
 conservation of Mexican temperate forests.
description: Three collection sites were established on each slope of the La
 Malinche National Park (12 in total). In each population, five 1,000
 m<sup>2</sup> circular plots were randomly located, separated
 by at least 50 m from edge to edge. Within each plot, vegetative tissue
 was collected from at least five individuals for each species, separated
 from one another by at least 30 m. For dehydration and further processing,
 all samples were stored in resealable bags with silica gel and labeled
 with the species name, population, cohort (adults, ≥10 m in height;
 seedlings, &lt; 0.5 m in height; Ramírez-Marcial et al. 2001), and
 geographic coordinates. Genomic DNA was extracted with
 the Plant Pro Kit (Qiagen). DNA was quantified with the PicoGreen
 fluorometric method using a NanoDrop™ ND 3300 fluorospectrometer (Thermo
 Scientific). Libraries were prepared in the Institute of Integrative
 Biology and Systems (IBIS) at the University of Laval by double digestion
 (ddRADSeq) using the enzymes PstI and MspI. Sequencing was obtained by the
 Genome Quebec Centre D'expertise et de Services through four lines of
 Illumina NovaSeq 6000 (PE150). Genotyping was carried
 out using the pipeline in Stacks v.2.62 (Catchen et al. 2013) with de novo
 alignment and applying the following criteria: exclusion of sites
 containing an indel (remove-indels), a minor allele count (mac) of 1, a
 maximum missing data per site (max-missing) of 0.2, inclusion of only
 biallelic sites displaying Hardy Weinberg Equilibrium, and only loci
 present in at least 90 % of individuals in each population (-r 0.10).
 Additional filtering was done with VCFtools v. 0.1.15 (Danecek et al.,
 2011), considering a minor allele frequency (MAF) of 0.01, a minimum mean
 depth (min-meanDP) of 10×, and a maximum mean depth (max-meanDP) of 196×
 for <em>A. religiosa</em> and 306× for <em>P.
 montezumae</em> (twice the mean depth obtained with the
 site-mean-depth command; Taylor et al, 2020, Yamasaki et a,l2020).
 Subsequently, we identified outliers through single-nucleotide
 polymorphism (SNP) scanning, using an alpha = 0.1, with PCAdapt v.4.3.3
 (Duforet-Frebourg et al. 2015; Luu et al. 2017) in the R program v.4.2.2
 (R Core Team 2022). Loci identified as adaptive were removed to retain
 only the neutral ones.
description: # Spatial genetic structure of two conifers in a highly human-modified
 landscape of central Mexico
 [https://doi.org/10.5061/dryad.9ghx3ffqw](https://doi.org/10.5061/dryad.9ghx3ffqw) There are two VCF files and two txt files with population data of each species (*Pïnus montezumae* and *Abies religiosa*). The VCF files are neutral SNPs obtained by double digestion (ddRADSeq) using the enzymes PstI and MspI. ## Description of the data and file structure VCF files (SNPAbiesNeutrales.recode.vcf and SNPPinusNeutrales.recode.vcf): *Abies religiosa* file has 7326 neutral snps from 48 individuals of nine populations of La Malinche National Park, Mexico. While *Pinus montezumae* file has 34,423 neutral snps from 70 individuals of 12 populations of La Malinche National Park, Mexico. These file can be used if it is correctly cited. TXT files (Abies48IndsCategories.txt and Pinus70IndsCategories.txt) : Each file has information about Id of each individual (INDIVIDUALS), population (POP), level of disturbance where they were collected (DIST), mountain's slope (SLOPE) and cohort (COHORT), i.e. adult or seed.