Data from: Genomic consequences and selection efficacy in sympatric sexual versus asexual kelps

Abstract
Genetic diversity can influence resilience and adaptative capacity of organisms to environmental change. Genetic diversity within populations is largely structured by reproduction, with the prevalence of asexual versus sexual reproduction often underpinning important diversity metrics that determine selection efficacy. Asexual or clonal reproduction is expected to reduce genotypic diversity and slow down adaptation through reduced selection efficacy, yet the evolutionary consequences of clonal reproduction remain unclear for many natural populations. Here, we examine the genomic consequences of sympatric sexual (haplodiplontic) and clonal morphs of the kelp Ecklonia radiata that occur interspersed on reefs in Hamelin Bay, Western Australia. Using genome-wide single nucleotide polymorphisms, we confirm significant asexual reproduction for the clonal populations, indicated by a significantly lower number of multi-locus lineages and higher intra-individual diversity patterns (individual multi-locus heterozygosity, MLH). Nevertheless, co-ancestry analysis and breeding experiments confirmed that sexual reproduction by the clonal morph and interbreeding between the two morphs is still possible, but varies among populations. One clonal population with long-term asexuality showed trends of decreased selection efficacy (increased ratio non- vs. synonymous gene diversities). Yet, all clonal populations showed distinct patterns of putative local adaptation relative to the sexual morph, possibly indicating maladaptation to local environmental conditions and high vulnerability of this unique clonal morph to environmental stress.  

Data
SNP datafile: HamelinClean.vcf
SNP input file used for population analysis
popmap file:  popmapHamelinClean.txt
population file used for analysis 
id = sampleID
site= siteID

摘要
遗传多样性能够影响生物对环境变化的韧性和适应性。种群内部的遗传多样性主要受繁殖方式的影响，而有无性繁殖与有性繁殖的普遍性往往构成了决定选择效力的关键多样性指标。预期无性或克隆繁殖会降低基因型多样性并减缓适应性，通过降低选择效力的方式，然而，对于许多自然种群而言，克隆繁殖的进化后果仍不明确。在本研究中，我们探讨了澳大利亚西部的哈梅林湾珊瑚礁上分布的紫菜（Ecklonia radiata）的同居有性（单倍体-二倍体）和克隆形态的基因组后果。通过全基因组单核苷酸多态性分析，我们证实克隆种群存在显著的无性繁殖，这体现在多座位谱系数量显著减少和个体间多样性模式（个体多座位点杂合度，MLH）显著增加。尽管如此，共同祖先分析和育种实验证实，克隆形态的有性繁殖以及两种形态间的杂交仍然是可能的，但这一现象在不同种群中存在差异。一个长期无性的克隆种群显示出选择效力降低（非同义与同义基因多样性比率增加）的趋势。然而，所有克隆种群与有性形态相比，均表现出独特的潜在局部适应性模式，这可能表明对当地环境条件的不适应，以及这种独特的克隆形态对环境压力的高度脆弱性。
数据
SNP 数据文件：HamelinClean.vcf
用于种群分析的 SNP 输入文件
popmap 文件：popmapHamelinClean.txt
用于分析的种群文件
id = 样本 ID
site= 站点 ID