Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984–1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711–7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.

中文翻译：

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对来自加勒比海巴拿马的人类捕获的海洋腹足动物（Strombus pugilis）的现代、考古和古生物学 DNA 分析

尽管存在从陆地蜗牛和海洋双壳贝壳中恢复古代 DNA 的协议，但尚未从古基因组学角度研究海洋海螺壳。我们首先展示了西印度战斗海螺Strombus pugilis的 623.7 Mbp 核基因组和 15.4 kbp 线粒体基因组的参考组装。接下来，我们详细介绍了一种从海螺壳中提取和测序 DNA 的方法，并将其应用于巴拿马博卡斯德尔托罗的海螺三个时期：最近被吃掉和丢弃（n  = 3），全新世晚期（984-1258 年之前 [BP ]) 考古中 ( n  = 5) 和中全新世 (5711–7187 BP) 古生物化石珊瑚礁 ( n = 5）。这些结果与从活捕获的组织和新鲜贝壳中提取的对照 DNA 进行比较 ( n  = 5)。使用高通量测序，我们能够获得S。 pugilis核序列从所有年龄段的贝壳中读取：活捕获的贝壳材料中每个样本的过滤读数高达 92.5 万条，现代废弃贝壳的 457 万条读数，考古贝壳的 1.21 万条读数，以及古生物贝壳中的 114 条读数。我们确认了从考古和古生物贝壳中回收的古代 DNA 的真实性，与现代贝壳相比，脱氨基驱动的错误掺入的平均频率高 5.7 倍，平均读取长度短 15%。读取也映射到S。 pugilis线粒体基因组，除了古生物壳外，所有样本类型的线粒体与核映射读数的比率一致。我们的方法可以应用于不同的考古遗址，以促进人类行为对软体动物进化生物学的长期影响的重建。