DOI: 10.5061/dryad.b5mkkwhg0
title: Genomic analyses point to a low evolutionary potential of prospective source populations for assisted migration in a forest herb

description: Climate change is increasingly impacting temperate forest ecosystems and
 many forest herbs might be unable to track the changing climate due to
 dispersal limitation. Forest herbs with a low adaptive capacity may
 therefore benefit from conservation strategies that mitigate dispersal
 limitation and evolutionary constraints, such as assisted migration.
 However, assisted migration strategies rarely consider evolutionary
 constraints of potential source populations that may jeopardize their
 success. In cases where climate adaptation is overshadowed by competing
 evolutionary processes, assisted migration is unlikely to support
 adaptation to future climates. Using a combination of population and
 landscape genomic analyses, we disentangled local adaptation drivers and
 quantified the adaptability and vulnerability to climate change of the
 self-incompatible deciduous forest herb Primula elatior. Southern
 populations displayed a sharp genetic turnover, and a considerable amount
 of local adaptation under diversifying selection was discovered. However,
 most of the outlier loci could not be linked to climate variables (71%)
 and were likely related to other local adaptation drivers, such as
 photoperiodism. Furthermore, specific adaptations to climate extremes,
 such as drought stress, could not be detected. This is in line with the
 typical occurrence of forest herbs in buffered climatic conditions, which
 can be expected to reduce selection pressures imposed by climate. Finally,
 populations in the south of the distribution area had increased
 sensitivity to climate change due to a reduced adaptive capacity and a
 moderate genetic offset, while central European populations were sensitive
 due to a high genetic offset. We conclude that assisted migration from
 southern source populations could bear significant risk due to nonclimatic
 maladaptation and a low adaptive capacity. Regional admixture and
 restoration of ecological connectivity to increase the adaptive capacity,
 and assisted range expansion to suitable habitat in the north might be
 more appropriate mitigation strategies.
description: All libraries for each
 sequencing lane were demultiplexed using the Illumina `bcl2fastq v.1.8.4´
 software (ILLUMINA, 2013). One mismatch or missing data point was allowed
 in the barcode read (5,343,298 ± 1,598,102 average total reads per sample
 ± SD). Sequencing adapter remnants were clipped
 from all raw reads, and reads with a final length &lt; 20 bases were
 discarded (2,671,608
 ± 799,040 average quality trimmed read pairs per sample
 ± SD). Adapter-clipped reads were quality trimmed
 by removing sequencing errors and trimming was focused on the 3'-end
 to get a minimum average Phred quality score of 10 over a window of ten
 bases (2,512,362
 ± 747,790 average adapter clipped read pairs per sample
 ± SD). Merged quality trimmed reads were error
 corrected (201,600,000 total read pairs) using `Musket v.1.0.6´ with a 21
 k-mer size for correction (Liu, Schröder, & Schmidt,
 2013). Furthermore,
 digital normalization of error-corrected reads (148,503,886 total reads)
 was performed with the `normalize_by_median.py´ script from `khmer v.1.1´
 with a k-mer size of 32 and a coverage cut-off of 80 (Crusoe et al., 2015).
 <em>De novo
 </em>assembly was
 performed with the `CLC Genomics Workbench v.8.0´ (QIAGEN, 2021). Gene discovery was performed with `Augustus
 v.3.1´ (Stanke, Diekhans,
 Baertsch, & Haussler, 2008) on the post-processed scaffolds. Complementary
 draft functional annotation of predicted peptides was performed with
 `InterProScan v.5.4-47.0´ (Jones et al., 2014). InterPro lookups for pathway and GO annotation
 were performed based on the predicted peptides (Camon et al., 2005). Quality trimmed reads were aligned against
 <em>Arabidopsis</em> as reference genome using `BWA-MEM
 v.0.7.12´ (Burrows-Wheeler Aligner; Li, 2013; Li & Durbin,
 2009). Variant discovery and genotyping of samples was
 executed with `Freebayes v.1.0.2-16´ with a diploid setting and reads with
 more than two mismatches were excluded from the dataset
 (Garrison & Marth,
 2012). Annotations of
 variant effects on annotated genes and transcripts were performed using
 `SnpEff v.4.31´ (Cingolani
 et al., 2012). The
 predicted genes and transcripts from the genome annotation were used to
 predict downstream functional effects of the
 variants.
description: This SNP dataset of <em>Primula elatior</em> was
 filtered for a minimum read depth of 5 per SNP and a minimum allele
 frequency across all samples of 5%, but was not yet filtered for missing
 data. The data Format is the VCF data format. More info about this data
 format can be found at https://samtools.github.io/hts-specs/VCFv4.2.pdf.