Inbreeding reduces fitness in spatially structured populations of a threatened rattlesnake

Small and fragmented populations are at high risk of local extinction, in part because of elevated inbreeding and subsequent inbreeding depression. A major conservation priority is to identify the mechanisms and extent of inbreeding depression in small populations. The eastern massasauga (Sistrurus catenatus) rattlesnake is listed as Federally Threatened in the United States, having experienced significant habitat fragmentation and concomitant population declines over the past 200 years. Here, we use long-term monitoring of two wild populations of eastern massasaugas in Michigan to estimate the extent of inbreeding in each population, identify mechanisms that generate inbreeding, and test for the impact of inbreeding on fitness. Using targeted genomic data and spatial coordinates of capture locations from over 1000 individuals, we find evidence of inbreeding and link inbreeding to spatial kinship structure within populations, possibly driven by limited dispersal. We reconstruct multi-ge..., , # Inbreeding reduces fitness in spatially structured populations of a threatened rattlesnake

**Contact person**:

Corresponding author:
Meaghan Clark, meaghaniclark[at]gmail[dot]com, [https://orcid.org/0000-0003-3297-8372](https://orcid.org/0000-0003-3297-8372)

#### Description of the data and file structure

For a visual representation of the analysis pipeline, see pipeline_viz.pdf

EMR_inbreeding_project.zip is a compressed directory that includes the following folders––

**data_inputs**/: Contains processed data input files for genetic, spatial, and pedigree analyses in R.

* BAR_LifeHistData_dupes.csv: Each row contains a set of IDs that reference technical duplicates of the same individual from the Barry County site
* CAS_captive_born.Robj: R object containing two objects. 
* 1: A list containing the numerical IDs of captive-born siblings. Name of each object in list is the ID of the mother. 
* 2: List of individual IDs of captive-born individuals who were never captured agai...,