How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population

Conservation introductions to islands and fenced enclosures are increasing as in situ mitigations fail to keep pace with population declines. Few studies consider the potential loss of genetic diversity and increased inbreeding if released individuals breed disproportionately. As funding is limited and post-release monitoring expensive for conservation programs, understanding how sampling effort influences estimates of reproductive variance is useful. To investigate this relationship, we used a well-studied population of Tasmanian devils (Sarcophilus harrisii) introduced to Maria Island, Tasmania. Pedigree reconstruction based on molecular data revealed high variance in number of offspring per breeder and high proportions of unsuccessful individuals. Computational subsampling of 20, 40, 60, and 80% of observed offspring resulted in inaccurate estimates of reproductive variance compared to the pedigree reconstructed with all sampled individuals. With decreased sampling effort, the proportion of inferred unsuccessful individuals was overestimated and the variance in number of offspring per breeder was underestimated. To accurately estimate reproductive variance, we recommend sampling as many individuals as logistically possible during the early stages of population establishment. Further, we recommend careful selection of colonising individuals as they may be disproportionately represented in subsequent generations. Within the conservation management context, our results highlight important considerations for sample collection and post-release monitoring during population establishment.

Methods
This upload contains the fastq files geneated via DArT-seqTM, scripts and metadata used to perform pedigree reconstruction and subsampling analysis presented in the Ecological Applications article "How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population" (EAP21-0107).

SNP calls were first made using the Stacks/2.0b pipeline from fastq files geneated via DArT-seqTM (uploaded here). The output from Stacks 2.0b (vcf. file) was further filtered in R (script available https://doi.org/10.1186/s12864-019-5806-y). All filtering parameters are presented in the Materials and Methods section of the article.

随着原位保护缓解措施无法跟上种群衰退的步伐，针对岛屿与围栏圈地的保护性引种项目正日益增多。鲜有研究关注当放归个体繁殖比例失衡时，种群可能面临的遗传多样性丧失与近交加剧风险。由于保护项目的资金有限，且放归后监测成本高昂，明晰采样力度如何影响繁殖方差的估算结果具有重要实践价值。
为探究这一关联，我们以引入至塔斯马尼亚州玛利亚岛的袋獾（Sarcophilus harrisii）种群为研究对象，该种群已得到充分研究。基于分子数据构建的谱系显示，每个繁殖个体的后代数量存在极高方差，且存在大量繁殖失败的个体。对20%、40%、60%和80%的观测后代进行计算性子采样后，相较于使用全部采样个体构建的谱系，繁殖方差的估算结果存在偏差。随着采样力度降低，被推断为繁殖失败的个体比例被高估，而单个繁殖个体的后代数量方差则被低估。为精准估算繁殖方差，我们建议在种群建立初期，在后勤条件允许的前提下尽可能多地采样个体。此外，建议对奠基种群个体进行审慎筛选，因为它们在后续世代中的繁殖占比可能失衡。在保护管理的框架下，本研究结果凸显了种群建立阶段采样与放归后监测的关键注意事项。

方法
本上传文件包含用于谱系构建与子采样分析的DArT测序（DArT-seq™）生成的fastq文件、脚本及元数据，对应发表于《生态应用》（Ecological Applications）的论文"How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population"（EAP21-0107）。
首先使用Stacks/2.0b流程，对本次上传的DArT测序生成的fastq文件进行单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点调用。随后在R语言中对Stacks 2.0b的输出结果（vcf文件）进行进一步过滤，相关脚本可访问https://doi.org/10.1186/s12864-019-5806-y获取。所有过滤参数均详见该论文的材料与方法部分。