Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities

Human-facilitated introductions of nonnative populations can lead to secondary contact between previously allopatric lineages, resulting in either homogenization of the lineages or stable hybrid zones that are maintained by pre-zygotic (e.g., behavioral) or post-zygotic (e.g., reduced hybrid fitness) reproductive barriers. We investigated patterns of gene flow between the native Sacramento Valley red fox (Vulpes vulpes patwin) and an introduced conspecific population of captive-bred (fur-farm) origin in California’s Central Valley. Considering their recent divergence (i.e., ~50 kya), we hypothesized that pre-zygotic mechanisms primarily impede gene flow, rather than post-zygotic barriers. Additionally, some genes originating in nonnative foxes may confer higher fitness in the currently human-dominated landscape resulting in selective introgression into the native population. Genetic analysis of 682 red foxes (255 native, 427 nonnative) at both mitochondrial (cytB + Dloop) and nuclear lo..., We obtained both scat (n = 195) and tissue (n = 490) samples as well as 4 hair and swab samples from red foxes in the native SVRF (n = 293) and nonnative ranges (n = 396). Samples were collected between 1982–2021 and many of them (n = 472) were first described in previous studies. Samples were obtained through non-invasive den and transect surveys, roadkill collection, live captures (following American Society of Mammalogy animal care guidelines and with University of California, Davis Animal Care and Use Committee approval, IACUC No.17860), and nonnative species removal programs in the case of the introduced red foxes., , # Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities

This dataset was used to generate results for the following manuscript which has been accepted in the Journal of Molecular Ecology (May 13th, 2024)

## Description of the data and file structure

This repository contains data and scripts required to recreate analyses in the manuscript *Maintenance of a narrow hybrid zone between native and introduced red foxes (Vulpes vulpes) despite conspecificity and high dispersal capabilities *which has been accepted into the Journal of Molecular Ecology as of May 13th, 2024.

The raw GBS sequencing data associated with this study can be found in the NCBI Sequence Read Archive under project number:

**PRJNA1069152** : Reduced-representation genotyping-by-sequencing of low-elevation red foxes in California

**Maintenance of a narrow hybrid zone between native and introduced red foxes despite conspecific...