Genomic analyses point to a low evolutionary potential of prospective source populations for assisted migration in a forest herb

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 ..., 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 < 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 `nor..., This SNP dataset of Primula elatior 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.Â

气候变化正日益对温带森林生态系统造成影响，多数森林草本植物受扩散限制，难以跟上气候变化的节奏。因此，适应能力较低的森林草本植物，或可从缓解扩散限制与进化约束的保护策略中获益，例如辅助迁移（assisted migration）。然而，辅助迁移策略极少考虑潜在源种群的进化约束，而这些约束可能会危及策略的实施成效。当气候适应被其他竞争性进化过程所掩盖时，辅助迁移将难以助力种群适应未来气候。本研究结合种群基因组学与景观基因组学分析，解析了自交不亲和落叶森林草本植物长莛报春（Primula elatior）的本地适应驱动因子，并量化了其对气候变化的适应性与脆弱性。南部种群呈现出显著的遗传更替现象，且存在大量本地适应特征……
每个测序泳道的所有文库均使用Illumina的`bcl2fastq v.1.8.4`软件（ILLUMINA, 2013）进行解多路复用。条码读取环节允许存在1个错配或缺失数据点，每个样本的平均总读段数为5,343,298 ± 1,598,102（±标准差）。从所有原始读段中剪切掉测序接头残留序列，最终长度小于20个碱基的读段将被丢弃，每个样本经质量修剪后的平均有效读对数量为2,671,608 ± 799,040（±标准差）。经接头剪切后的读段将进行质量修剪：通过移除测序错误，且修剪操作聚焦于3'端，以在10个碱基的窗口内获得至少10的平均Phred质量值，每个样本的平均接头剪切后读对数量为2,512,362 ± 747,790（±标准差）。将合并后的质量修剪读段进行错误校正（总读对数量为201,600,000），校正工具为`Musket v.1.0.6`，k-mer大小设置为21（Liu, Schröder, & Schmidt, 2013）。此外，使用`nor...`工具对经错误校正的读段（总读段数为148,503,886）进行数字化归一化处理。
本长莛报春（Primula elatior）的单核苷酸多态性（SNP）数据集已进行过滤：每个SNP的最低测序深度为5，所有样本中的最小等位基因频率为5%，但尚未针对缺失数据进行过滤。该数据集采用变异识别格式（VCF）格式，有关该格式的详细信息可参考https://samtools.github.io/hts-specs/VCFv4.2.pdf。