10.5061/DRYAD.Q83BK3JG0
Zonana, David
0000-0002-1599-8913
University of Colorado Boulder
Gee, Jennifer
0000-0001-8497-7262
University of California, Riverside
Breed, Michael
0000-0002-4039-8354
University of Colorado Boulder
Doak, Daniel
University of Colorado Boulder
Dynamic shifts in social network structure and composition within a
breeding hybrid population
Dryad
dataset
2020
reproductive barriers
parentage analysis
phenotypic assortment
network rewiring
social network dynamics
University of Colorado Boulder, EBIO Department*
University of Colorado Boulder, Museum of Natural History*
American Society of Naturalist
https://ror.org/01hvxhn04
Pasadena Audubon Society*
American Museum of Natural History
https://ror.org/03thb3e06
American Ornithological Society
https://ror.org/03wy7n216
Anza Borrego Foundation*
Achievement Rewards for College Scientists Foundation
https://ror.org/054awkm93
Animal Behavior Society
https://ror.org/031nh9x49
Society for the Study of Evolution
https://ror.org/057kr0a20
Wilson Ornithological Society
https://ror.org/03cqty937
Sea & Sage Audubon Society*
University of Colorado Boulder, EBIO Department
University of Colorado Boulder, Museum of Natural History
Pasadena Audubon Society
Anza Borrego Foundation
Sea & Sage Audubon Society
2020-08-13T00:00:00Z
2020-08-13T00:00:00Z
en
https://doi.org/10.5061/dryad
9992956845 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.