Evidence of extensive home range sharing among mother-daughter bobcat pairs in the wildland-urban interface of the Tucson Mountains

Urbanization impacts the structure and viability of wildlife populations. Some habitat generalists, such as bobcats (Lynx rufus), maintain populations at the intersection of wild and urban habitats (wildland urban interface, WUI), but impacts of urbanization on bobcat social structure are not well understood. Although commonly thought to establish exclusive home ranges among females, instances of mother-daughter home range sharing have been documented. We combined GPS localities with genomic relatedness inferences from double-digest restriction site associated DNA sequencing (ddRADseq) to investigate mother-daughter home range sharing in bobcats (n = 38) at the WUI in the Tucson Mountains, Arizona, USA. We found the highest relatedness among females, which showed stronger isolation by distance than males and the population as a whole. Using mother-daughter relationships inferred from pedigree reconstruction, we found extensive mother-daughter home range sharing, compared to other female..., This dataset contains double digest restriction-site associated DNA sequencing data from 38 bobcats (Lynx rufus) sampled between 2020 and 2023 at the wildland-urban interface of the Tucson Mountains, Arizona, USA. Initial processing of raw sequencing data began with removal of PCR duplicates with the Stacks v. 2.60 clone_filter module, followed by trimming an additional five bp from the 5’ ends of the reverse reads using Trimmomatic v. 0.39 (to expose the EcoRI cut site at the front of the read). Finally, we demultiplexed, quality filtered with default settings, and filtered for missing restriction enzymes sites (for enzymes NlaIII and EcoRI-HF) and adapter contamination using the Stacks process_radtags module (using options -c -q -r). Each individual has four resulting fastq (.fq) files in the dataset, including paired reads (files ending in \".1.fq.gz\"/\".2.fq.gz\") and reads remaining after the other read from a read pair was discarded (files ending in \".rem.1.fq.gz\"/\".rem.2.fq.gz\"). Th..., , # Evidence of extensive home range sharing among mother-daughter bobcat pairs in the wildland-urban interface of the Tucson Mountains

[https://doi.org/10.5061/dryad.7h44j104h](https://doi.org/10.5061/dryad.7h44j104h)

## Description of the data and file structure

This dataset contains double digest restriction-site associated DNA sequencing data from 38 bobcats (*Lynx rufus*) sampled between 2020 and 2023 at the wildland-urban interface of the Tucson Mountains, Arizona, USA. Initial processing of raw sequencing data began with removal of PCR duplicates with the Stacks v. 2.60 clone_filter module, followed by trimming an additional five bp from the 5’ ends of the reverse reads using Trimmomatic v. 0.39 (to expose the *Eco*RI cut site at the front of the read). Finally, we demultiplexed, quality filtered with default settings, and filtered for missing restriction enzymes sites (for enzymes *Nla*III and *Eco*RI-HF) and adapter contamination using the Stacks process_radtags module (using ...

城市化会对野生动物种群的结构与存续能力造成影响。部分栖息地广适物种，如短尾猫（*Lynx rufus*），可在野生与城市栖息地的交错地带——城乡交错带（wildland urban interface, WUI）——维持种群存续，但目前学界对城市化如何影响短尾猫的社会结构仍缺乏充分认知。尽管普遍认为雌性短尾猫会建立排他性家域，但已有文献记录了母女共享家域的案例。本研究结合GPS定位数据与双酶切限制性位点相关DNA测序（double-digest restriction site associated DNA sequencing, ddRADseq）得到的基因组亲缘关系推断结果，对美国亚利桑那州图森山脉城乡交错带的38只短尾猫（n=38）展开母女共享家域相关研究。研究发现雌性个体间的亲缘关系最高，且雌性的距离隔离效应强于雄性个体及整个种群。通过家系重建推断得到的母女关系显示，相较于其他雌性个体……本数据集包含2020年至2023年间，于美国亚利桑那州图森山脉城乡交错带采集的38只短尾猫（*Lynx rufus*）的双酶切限制性位点相关DNA测序数据。

原始测序数据的初始处理流程如下：首先使用Stacks v2.60的clone_filter模块去除PCR重复序列，随后使用Trimmomatic v0.39对反向测序reads的5'端额外修剪5个碱基，以暴露reads前端的*Eco*RI酶切位点。最后，使用Stacks的process_radtags模块（参数为`-c -q -r`）进行解多重处理、默认参数的质量过滤，同时过滤缺失*Nla*III与*Eco*RI-HF两种限制性酶切位点的序列及接头污染。本数据集内每个个体对应4个最终得到的fastq（.fq）压缩文件，包括成对测序reads（文件后缀为".1.fq.gz"与".2.fq.gz"），以及读对中一条reads被丢弃后剩余的reads（文件后缀为".rem.1.fq.gz"与".rem.2.fq.gz"）。……

# 图森山脉城乡交错带短尾猫母女家域共享的实证证据
[https://doi.org/10.5061/dryad.7h44j104h](https://doi.org/10.5061/dryad.7h44j104h)

## 数据与文件结构说明
本数据集包含2020年至2023年间，于美国亚利桑那州图森山脉城乡交错带采集的38只短尾猫（*Lynx rufus*）的双酶切限制性位点相关DNA测序数据。原始测序数据的初始处理流程如下：首先使用Stacks v2.60的clone_filter模块去除PCR重复序列，随后使用Trimmomatic v0.39对反向测序reads的5'端额外修剪5个碱基，以暴露reads前端的*Eco*RI酶切位点。最后，使用Stacks的process_radtags模块（参数为`-c -q -r`）进行解多重处理、默认参数的质量过滤，同时过滤缺失*Nla*III与*Eco*RI-HF两种限制性酶切位点的序列及接头污染。