DOI: 10.5061/dryad.q83bk3jg0
title: Dynamic shifts in social network structure and composition within a breeding hybrid population

description: 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
description: 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).
description: This repository contains raw, short read ddRAD sequence data from
 California (<em>Callipepla californica</em>) and Gambel's
 quail (<em>Callipepla gambelii</em>) 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.