1. Mating behavior and the timing of reproduction can inhibit genetic exchange between closely related species; however, these reproductive barriers are challenging to measure within natural populations. Social network analysis provides promising tools for studying the social context of hybridization, and the exchange of genetic variation, more generally. 2. We test how social networks within a hybrid population of California (Callipepla californica) and Gambel’s quail (Callipepla gambelii) change over discrete periods of a breeding season. We assess patterns of phenotypic and genotypic assortment, and ask whether altered associations between individuals (association rewiring), or changes to the composition of the population (individual turnover) drive network dynamics. We use genetic data to test whether social associations and relatedness between individuals correlate with patterns of parentage within the hybrid population. 3. To achieve these aims, we combine RFID association data, phenotypic data, and genomic measures with social network analyses. We adopt methods from the ecological network literature to quantify shifts in network structure and to partition changes into those due to individual turnover and association rewiring. We integrate genomic data into networks as node-level attributes (ancestry) and edges (relatedness, parentage) to test links between social and parentage networks. 4. We show that rewiring of associations between individuals that persist across network periods, rather than individual turnover, drives the majority of the changes in network structure throughout the breeding season, and that the traits involved in phenotypic/genotypic assortment were highly dynamic over time. Social networks were randomly assorted based upon genetic ancestry, suggesting weak behavioral reproductive isolation within this hybrid population. Finally, we show that the strength of associations within the social network, but not levels of genetic relatedness, predict patterns of parentage. 5. Social networks play an important role in population processes such as the transmission of disease and information, yet there has been less focus on how networks influence the exchange of genetic variation. By integrating analyses of social structure, phenotypic assortment, and reproductive outcomes within a hybrid zone, we demonstrate the utility of social networks for analyzing links between social context and gene flow within wild populations. 08-Jul-2020

We extracted DNA from blood samples and museum tissues using Qiagen DNEasy Blood and Tissue kits (Qiagen, Hilden, Germany). Double-digest restriction associated sequencing (ddRAD-seq) library preparations and sequencing were performed by RTL Genomics (Lubbock, TX). Briefly, 500ng of each sample were digested using restriction enzymes Sbfl and Msp1, and placed in a thermal cycler set to 37°C for three hours and held at 4°C overnight. Samples underwent a 1.5x AMPure cleanup, were quantified using a Quibt 2.0 Fluorometer and DNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA), and normalized. Samples were ligated with adapters overnight at 4°C, followed by an additional 1.5x AMPure cleanup, and transferred to a PCR plate containing unique Illumina tag barcodes. Individual libraries were pooled, fragment analyzed, and fragment size selected (400-700bp) using BluePippin (Sage Science, Beverly, MA). Samples were sequenced on an Illumina HiSeq 2000 platform with paired-end, 125bp reads. Several samples sequenced at low coverage, and were re-sequenced with paired-end 125bp reads on a single NextSeq run. Reads were combined across runs and demultiplexed using BaseSpace software (Illumina, San Diego, CA).

This repository contains raw, short read ddRAD sequence data from California (Callipepla californica) and Gambel's quail (Callipepla gambelii) from both museum specimens and wild-caught individuals from a hybrid zone between the two species in the deserts and mountains of Southern California. The accompanying spreadsheet contains information on the museum source or population from which each sample originated.