DOI: 10.5061/dryad.gxd2547t6
title: Data from: Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán

description: Climate change and land use change are two main drivers of global
 biodiversity decline, decreasing the amount of genetic diversity that
 populations harbor and altering the patterns of local
 adaptation.  Methods in landscape genomics allow measuring the
 effect of these anthropogenic disturbances on the adaptation of
 populations. However, both factors have rarely been considered
 simultaneously. We modeled the spatial turnover in allele frequencies of
 19 localities of Pinus leiophylla across the Avocado Belt in Michoacán
 state, Mexico which could change under climate change and land use change
 scenarios, in addition to evaluating assisted gene flow strategies and
 connectivity metrics across the landscape to identify priority
 conservation areas. We found that localities at the center-east regions
 would be more vulnerable to climate change, while localities in the west
 area will be more threatened by actions of land use change. However,
 assisted gene flow actions could reduce their risk of extinction for both
 scenarios. Connectivity patterns will also be modified by future habitat
 loss, with the central and eastern parts having the highest connectivity
 values. These results show that the areas with the highest priority for
 conservation are in the eastern zones, which include the Monarch Butterfly
 Biosphere Reserve. This work is useful as a framework that incorporates
 distinct layers of information to provide a robust representation of the
 response of populations to future anthropogenic disturbances.
description: Our sampling was conducted in the “Avocado Belt”, in the state of
 Michoacán, México. We sampled 77 individuals from 19 populations of
 <em>Pinus leiophylla.</em> Genomic libraries were created
 using the ddRAD-Seq method.  Briefly, genomic DNA of
 each sample was digested using the restriction enzymes <em>Pstl
 </em>and <em>MseI, </em>and an adapter was ligated to
 the DNA fragments. The adapter-ligated fragments were sequenced using
 Illumina NovaSeq 6000. The sequenced samples were demultiplexed and
 trimmed for further analysis. A <em>de
 novo</em> RAD reference genome was constructed using the individual
 that had the highest number of unique RAD sequences. Next, we used custom
 scripts to cluster identical sequences. The assembly for the reference
 individual was realigned against itself using BWA (Li & Durbin,
 2009). BOWTIE (Langmead <em>et al.</em>, 2009) was then used
 to align the reads of each individual to the RAD reference genome.
 SAMTOOLS (Li <em>et al.</em>, 2009) and custom scripts were
 used to detect and filter SNPs that had a minimum sequencing depth per
 sample of 15x, individual per locus genotype quality scores of at least 20
 and a minimum of 10x sequence coverage. Subsequently,
 we used PLINK v1.9 (Purcell <em>et al.</em>, 2007) and
 vcftools v0.1.16 (Danecek <em>et al.</em>, 2011) to retain
 diallelic SNPs that were in Hardy-Weinberg equilibrium, had minor allele
 frequencies (MAF) ≥ 0.025 and had less than 20% of missing data. We also
 removed SNPs that were in linkage disequilibrium (LD &lt; 0.5) within
 a window size of 50 bp and a window shift of 5 (Purcell <em>et
 al.</em>, 2007). We used HDplot (McKinney <em>et
 al.</em>, 2017) to remove possible paralogs. We removed all regions
 that had observed heterozygosities (<em>Ho</em>) greater than
 0.5 and a <em>D</em> value outside the range of -15 and 15,
 which could indicate potentially duplicate loci due to deviation of
 allelic ratios expectation. After these filtering procedures we obtained
 3660 SNPs. 
description: # **Data from: Local adaptation of Pinus leiophylla under climate and land
 use change models in the Avocado Belt of Michoacán** #####
 *Pinus\_leiophylla*\_landscape\_genomics
 [https://doi.org/10.5061/dryad.gxd2547t6](https://doi.org/10.5061/dryad.gxd2547t6) This is a .vcf of 77 individuals from 19 *Pinus leiophylla* locations collected throughout the avocado belt in the state of Michoacán, México. We used the ddRAD-Seq protocol and sequenced using Illumina NovaSeq 6000. ## Description of the data and file structure **ld_relaxed_90k.vcf.recode**: This .vcf file contain 3660 SNPs sites from  77 individuals from 19 *Pinus leiophylla* locations. At each site, we randomly chose 2-5 adult trees. The locations are identified from A-U. Locations "O" and "P" were excluded. We used PLINK v1.9 (Purcell *et al.*, 2007) and vcftools v0.1.16 (Danecek *et al.*, 2011) to retain diallelic SNPs that had minor allele frequencies (MAF) ≥ 0.025 and had less than 20% of missing data. We also removed SNPs that were in linkage disequilibrium (LD &lt; 0.5) within a window size of 50 bp and a window shift of 5 (Purcell *et al.*, 2007). We used HDplot (McKinney *et al.*, 2017) to remove possible paralogs. We removed all regions that had observed heterozygosities (*H*O) greater than 0.5 and a *D* value outside the range of -15 and 15, which could indicate potentially duplicate loci due to deviation of allelic ratios expectation. After these filtering procedures we obtained the 3660 SNPs mentioned above. ## Code/Software **Genetic_diversity.R**: Script to obtainobtain the per SNP site and mean observed heterozygosity (*H*O), gene diversity (*H*S), the inbreeding coefficient (*F*IS) per locality, the number of private alleles and the genetic differentiation among localities using the Weir and Cockerham *F*ST **LFMM.R**: Script to perform the LFMM analysis **GF.R**: Script to perform the GF and genomic offsets analysis