DOI: 10.5061/dryad.7h44j104h
title: Data from: Evidence of extensive home range sharing among mother-daughter bobcat pairs in the wildland-urban interface of the Tucson Mountains

description: 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 females. Every
 mother identified as having at least one daughter, shared home ranges with
 one daughter, while other confirmed daughters established adjacent home
 ranges. Our results provide substantial support for the mother-daughter
 home range sharing hypothesis, as well as evidence of spatiotemporal
 overlap between mothers and daughters, adding to the body of research
 complicating the solitary felid paradigm. These results additionally
 challenge the notion of home range partitioning by prior rights land
 tenure, suggesting a role of matrilineal land tenure in home range
 establishment of daughters. Habitat fragmentation due to human population
 growth and urbanization thus has the potential to alter landscape genetic
 structure and social dynamics in bobcats.
description: This dataset contains double digest restriction-site associated
 DNA sequencing data from 38 bobcats (<em>Lynx rufus</em>)
 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
 <em>Eco</em>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 <em>Nla</em>III
 and <em>Eco</em>RI-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"). The
 population map file used to process the fastq files with the Stacks
 denovo_map module is also included. This dataset includes fastq files for
 6 individuals later filtered out due to missing data (these are denoted
 with "yes" in the "Filtered_out" column of the csv
 file). The final SNP set is included here as a .vcf file, along with a
 .csv file containing relevant sample metadata and the life history data
 used for pedigree reconstruction with Sequoia.
description: # 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 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"). The population map file used to process the fastq files with the Stacks denovo_map module is also included. This dataset includes fastq files for 6 individuals later filtered out due to missing data (these are denoted with "yes" in the "Filtered_out" column of the csv file). The final SNP set is included here as a .vcf file, along with a .csv file containing relevant sample metadata and the life history data used for pedigree reconstruction with Sequoia. ### Files and variables #### File: populations.snps.vcf **Description:** This is the final set of 27,922 SNPs (in 32 individuals) output from Stacks v. 2.60 *populations*, after filtering the initial SNP set with Plink v. 1.9 (--geno 0.25, --mind 0.5, and --maf 0.05). The --write-random-snp flag was used. #### File: BIT\_popmap.txt **Description:** This text file is used for running the Stacks *denovo_map* pipeline (or the standalone *populations* module) to generate the SNP dataset. ##### Variables * Sample ID: Sample IDs, as given in the BIT_metadata.csv file. * Population: All are denoted as "BIT" (members of the "Bobcats in Tucson" study population). #### File: BIT\_metadata.csv **Description:** This file contains the ID, sampling date, capture location, sex, and sample type for each sample. The last column denotes whether the individual was excluded from the final dataset through filtering with Plink. ##### Variables * ID: Individual bobcat identifiers * Collection_Date: The date samples were collected * Latitude: Latitude for location of bobcat capture/sample collection * Longitude: Longitude for location of bobcat capture/sample collection * Sex: Sex of individual bobcat ('F' denotes female, and 'M' denotes male) * Sample_Type: Source of DNA used in the ddRAD library (blood or buccal swab) * Filtered_out: 'yes' indicates samples excluded with Plink filtering due to too much missing data. 'no' indicates samples present in the final SNP dataset (i.e. the vcf file included here) #### File: BIT\_LifeHist\_sequoia.txt **Description:** This is the Life History data used as input for pedigree construction with Sequoia. ##### Variables * IndID: Sample ID as given in the BIT_metadata.csv file * Sex: Sex of individuals denoted as '1' = female and '2' = male * Birth Year: Estimated or known birth year if available (if not, 'NA') * BY.min: Estimated minimum birth year if available (if not, 'NA') * BY.max: Estimated maximum birth year if available (if not, 'NA') #### File: Lynx\_rufus\_ddRADseq.tar.gz **Description:** This contains the full set of fastq files for each individual, after demultiplexing with *Stacks* process_radtags. 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"). ## Code/software The fastq files provided here can be analyzed with Stacks (Stacks v. 2.60 was specifically used here), although similar SNP calling software (such as ipyrad) could also be used. The vcf file can be analyzed with various programs (such as vcftools) or converted to other common genomic data formats if needed (using a program such as PGDspider).