Genomic insights from natural history collections reveal cryptic speciation in coral-guard crabs (family: Trapeziidae)

Mutualistic relationships such as the one between Trapezia crabs and coral colonies are common in reef organisms and play a crucial role in coral resilience and resistance to climate-induced stressors, yet very little is known about the taxonomic diversity and evolutionary history of the species involved. Despite being essential actors of coral reefs and threatened by the ongoing degradation of their habitat, little genetic information is available for Trapezia crabs, including the exact number of species and their relationships. To overcome this limitation, we sampled Natural History collections, an important and underutilized source of genomic data. We used a novel approach optimized for degraded DNA, to generate high-quality genomic data from a combination of 166 museum tissues and freshly collected samples and recovered a strongly supported phylogeny of the Trapezia genus, clarifying species relationships of a majority of taxa and suggesting the potential division of Trapezia into t...,

Samples were collected from the reefs of Guam and museum repositories from the Florida Museum of Natural History and the Paris Museum National d’Histoire Naturelle. DNA was extracted and sent for Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di®, Enoki & Takeuchi 2019) sequencing at the University of California, Davis. Reads were processed and SNP matrices were created in STACKS v2.60 (Catchen et al. 2011, 2013).

, , # Genomic insights from Natural History Collections reveal cryptic speciation in coral-guard crabs (family: Trapeziidae)

[https://doi.org/10.5061/dryad.x0k6djhtr](https://doi.org/10.5061/dryad.x0k6djhtr)

## Data description

**SNP Matrices - created in STACKS v2.60 (Catchen et al. 2011, 2013)**

Short reads were demultiplexed, adaptors were removed, and sequences were trimmed to 100 bp using process_shortreads. To optimize STACKS parameters, five random samplings of three individuals each were used to trial M = 1-9, as in Jeffries et al. 2016. Once M was set, all samples were included to trial n = 3-5, allowing only for SNPs present in 80% of samples (Paris et al. 2017). The remaining parameters were kept at default settings (m = 3, r = 0.5, and min-maf = 0.05). This assessment was repeated for both the phylogeny and phylogeography datasets.

**populations_allsp.vcf:**

SNP matrix of all samples included in phylogenetic analyses (species inc. *Trapezia lutea, T. guttata, T. serenei, ...,

梯形蟹属（Trapezia）与珊瑚群落之间的互利共生关系，是礁栖生物中极为常见的物种互作类型，对珊瑚的抗逆性及抵御气候诱导胁迫的能力发挥着关键作用。然而目前学界对该类群所涉及物种的分类多样性与演化历史仍知之甚少。尽管梯形蟹是珊瑚礁生态系统的核心功能类群，但其栖息地正持续退化，该类群面临严重的生存威胁；同时目前可供研究的梯形蟹遗传信息极为匮乏，连确切的物种数量与物种间演化关系都尚未明确。

为突破这一研究瓶颈，我们利用自然历史馆藏标本这一重要但尚未被充分开发的基因组数据来源开展采样。我们开发了针对降解DNA优化的全新实验方案，从166份馆藏组织样本与新鲜采集样本的混合组中获取了高质量基因组数据，并重建了支持度极高的梯形蟹属系统发育树，阐明了多数类群的物种间演化关系，同时提出将梯形蟹属划分为...的潜在分类方案。

样本采集自关岛的珊瑚礁，以及美国佛罗里达自然历史博物馆（Florida Museum of Natural History）、法国国家自然历史博物馆（Muséum National d'Histoire Naturelle）的馆藏标本库。提取DNA后，送至美国加州大学戴维斯分校，采用随机扩增子直接测序分型技术（Genotyping by Random Amplicon Sequencing-Direct, GRAS-Di®，Enoki & Takeuchi 2019）进行测序。对测序下机reads进行质控处理，并通过STACKS v2.60软件（Catchen et al. 2011, 2013）构建单核苷酸多态性（Single Nucleotide Polymorphism, SNP）矩阵。

# 基于自然历史馆藏的基因组研究揭示护珊瑚蟹（梯形蟹科Trapeziidae）的隐存物种形成
[https://doi.org/10.5061/dryad.x0k6djhtr](https://doi.org/10.5061/dryad.x0k6djhtr)

## 数据描述
**单核苷酸多态性矩阵——基于STACKS v2.60软件构建（Catchen et al. 2011, 2013）**
使用process_shortreads工具对双端reads进行拆分（demultiplex）、接头序列去除，并将序列修剪至100 bp。为优化STACKS软件的参数，我们参照Jeffries等人2016年的方法，随机选取5组、每组3个个体的样本，对M值（1-9）进行参数测试。确定M值后，纳入全部样本对n值（3-5）进行测试，仅保留在80%以上样本中存在的单核苷酸多态性位点（Paris et al. 2017）。其余参数保持默认设置（m=3、r=0.5、min-maf=0.05）。上述参数优化流程同时适用于系统发育与系统地理数据集。

**populations_allsp.vcf：**
该文件包含系统发育分析中纳入的全部样本的SNP矩阵，涉及物种包括黄体梯形蟹（Trapezia lutea）、斑点梯形蟹（T. guttata）、塞氏梯形蟹（T. serenei）等