Data from: A cost-and-time effective procedure to develop SNP markers for multiple species: a support for community genetics

1.Multi‐species population genetics is an emerging field that provides insight relevant to conservation biology and community ecology. However, to date, this approach is limited to species with available genetic resources. The use of thousands of single nucleotide polymorphism (SNP) markers developed from recent genotyping‐by‐sequencing (GBS) technologies is a roadmap for the study of non‐model species, but remains cost prohibitive when several, distantly related species are involved.

2.We aimed to overcome this issue by using a single HiSeq3000 run of restriction‐site associated DNA sequencing (RAD‐Seq) to retrieve SNP markers for 40 diverse species including plants, invertebrates, fish and mammals. We developed a Python‐based pipeline to isolate ~100‐500 high‐quality SNP markers for each species that could be genotyped through classical PCR amplification methods. To assess the quality of these markers, we validated our approach on ~160 of the characterized SNPs for each of 18 Neotropical fish species from the river Maroni (French Guiana, South America), using the MassARRAY iPLEX platform from Agena Bioscience (San Diego, CA, USA).

3.A run of the pipeline applying stringent filtering parameters enabled the successful design of between 130 and 3492 SNP markers for 30 of the 40 study species. Relaxing pipeline parameters allows for an increase in the number of detected SNPs. Across the 18 species from French Guiana, an average of 85% of markers were successfully amplified, polymorphic, and scored in ≥90% of individuals (~200 individuals per species). The great majority (>98%) of these markers were at Hardy‐Weinberg equilibrium in each sampling site from the river Maroni.

4.This SNP discovery was performed at the cost of ~$US110 for each of the 40 species. Genotyping was performed at the cost of ~$US6000 for each of the 18 fish species with an average of 200 individuals per species. This strategy was found cost‐and‐time efficient to develop hundreds of SNP markers for a large range of non‐model species, which can be used to investigate ecological and evolutionary questions that do not require whole‐genome coverage.

1. 多物种种群遗传学（Multi‐species population genetics）是一门新兴研究领域，可为保护生物学与群落生态学提供重要研究视角。但迄今为止，该研究方法仅适用于具备可用遗传资源的物种。依托最新测序分型（genotyping‐by‐sequencing, GBS）技术开发的数千个单核苷酸多态性（single nucleotide polymorphism, SNP）标记，为非模式物种的研究提供了可行路线图，但当涉及多个远缘物种时，该方案仍存在成本过高的问题。
2. 本研究旨在通过单次HiSeq3000测序的限制性位点相关DNA测序（restriction‐site associated DNA sequencing, RAD‐Seq），为涵盖植物、无脊椎动物、鱼类及哺乳类在内的40个不同类群物种获取SNP标记，以此解决上述成本问题。我们开发了一套基于Python的分析流程，可从每个物种中筛选获得约100~500个高质量SNP标记，这些标记可通过经典PCR扩增技术完成基因分型。为评估标记质量，我们使用美国加利福尼亚州圣地亚哥Agena Bioscience公司的MassARRAY iPLEX基因分型平台，对来自南美洲法属圭亚那马罗尼河的18个新热带区鱼类物种的每个物种约160个已注释SNP进行了方法验证。
3. 采用严格过滤参数运行该分析流程后，成功为40个研究物种中的30个设计出130~3492个SNP标记。放宽流程参数则可提升检测到的SNP数量。针对来自法属圭亚那的18个物种，平均85%的标记可成功扩增、具备多态性，且在≥90%的个体（每个物种约200个个体）中可完成分型。在马罗尼河的每个采样点中，绝大多数（>98%）此类标记均符合哈迪-温伯格平衡（Hardy‐Weinberg equilibrium）。
4. 本研究的SNP发掘环节，每个物种的成本约为110美元。针对18个鱼类物种的基因分型环节，每个物种（平均200个个体）的成本约为6000美元。该策略被证实兼具成本与时间效益，可针对大量非模式物种开发数百个SNP标记，用于开展无需全基因组覆盖范围的生态学与进化学研究。