Dataset DOI: 10.5061/dryad.w3r228189

Description of the data and file structure

We collected articles using a standardized search in R. We created a custom script that searched and pulled publications from the PubMed database. Search terms "hybrid swarm" and "biology" were used to provide bounds for the PubMed database search and we modified our query as to not include the word "particle". In each of our two searches, we pulled 74 articles, following the default batch size in the example we worked from. The search provided key information such as the title, publishing journal, author list, and date of publication, which were then used to find and download the full articles. Each article was read independently by two different readers and assessed for fit in the scope of this review. A total of 6 different readers were involved in reading and assessing all articles. If the data collected by the two readers for a single article did not match, any differences were manually evaluated and reconciled by an additional reader.

Files and variables

File: hybrid_swarm_pubmed.R

Description: Script used to conduct the PubMed search and pull articles. 

File: hybridswarm_plotting.R

Description: Script used for creating the plots in Figures 2 and 3.

File: hybridswarm_-_Cleaned.csv

Description: Cleaned version of the raw data. NA values indicate that either the field wasn't relevant to the paper and therefore wasn't evaluated by the reader, or that the information was unclear in the paper and therefore not recorded by the reader. 

Variables

• Papercode: A code to refer to the papers with, which combines the first author's last name and the last two digits of the year of publication. 
• Year: Year of publication. 
• Readers: How many readers read and reviewed this paper. 
• Relevant: Papers were deemed either relevant or not to hybridization in an evolutionary biology context. 
• ActiveHybSwarm: Papers were deemed to be either describing an ongoing hybrid swarm or not. Articles were given a "no" in this category for one of two reasons: either the authors stated that the organisms in their study system were descended from a hybrid swarm or that their system could become a hybrid swarm in the future, rather than actively existing as one during the time of study.
• GeneticEvidence: Whether the paper uses genetic evidence to describe the study system. 
• PhenotypicEvidence: Whether the paper uses phenotypic evidence to describe the study system.
• GenoAndPhenoEvidence: Whether the paper uses both genetic and phenotypic evidence to describe the study system.
• BehaviouralEvidence: Whether the paper uses behavioural evidence to describe the study system.
• SpatialEvidence: Whether the paper uses spatial evidence to describe the study system.
• TranscriptomicEvidence: Whether the paper uses transcriptomic evidence to describe the study system.
• PhysiologicalEvidence: Whether the paper uses physiological evidence to describe the study system.
• Genus: The genus described in the paper. 
• OrganismType: The organism type described in the paper. 
• Nspecies: The number of species described in the paper. 
• Nind: The number of individuals described in the paper. 
• Nloci: The number of loci analyzed in the paper. 
• Locations: The number of sampling sites described in the paper. 
• YearsofHybBin: Which bin used to describe the length of time the hybrid swarm has been ongoing for. 
• StartofHybBin: Which bin used to describe the start time of the hybrid swarm.
• UsedMicrosatellites: Whether the paper uses microsatellite data. 
• UsedSNPs: Whether the paper uses SNP data. 
• UsedmtDNA: Whether the paper uses mitochondrial data. 
• UsedAFLP: Whether the paper uses amplified fragment length polymorphism data. 
• UsednrDNA: Whether the paper uses nuclear data. 
• UsedcpDNA: Whether the paper uses chloroplast data. 
• UsedddRAD: Whether the paper uses double digest restriction-site associated DNA data. 
• F1Present: Whether the paper shows evidence for the presence of F1 hybrids in the study system. 
• F2orLaterPresent: Whether the paper shows evidence for the presence of F2 or later generation hybrids in the study system. 
• BackcrossPresent: Whether the paper shows evidence for the presence of backcrosses in the study system. 
• Anthropogenic: Whether the paper shows evidence for anthropogenic disturbance in the study system. 
• Introduced: Whether the paper shows evidence for species introduction in the study system. 
• Disturbance: Whether the paper shows evidence for non-anthropogenic disturbance in the study system. 
• DataAvailable: Whether the raw data for the paper has been made publicly available. 

File: hybridswarm_-_RawData.csv

Description: Raw data on each paper pulled in the PubMed search, as evaluated by each reader. NA values indicate that either the field wasn't relevant to the paper and therefore wasn't evaluated by the reader, or that the information was unclear in the paper and therefore not recorded by the reader. 

Variables

• Papercode: A code to refer to the papers with, which combines the first author's last name and the last two digits of the year of publication. 
• Title: Title of the paper. 
• Year: Year of publication. 
• Reader: Who read the paper and filled in this row of data. 
• Relevant: Papers were deemed either relevant or not to hybridization in an evolutionary biology context. 
• ActiveHybSwarm: Papers were deemed to be either describing an ongoing hybrid swarm or not. Articles were given a "no" in this category for one of two reasons: either the authors stated that the organisms in their study system were descended from a hybrid swarm or that their system could become a hybrid swarm in the future, rather than actively existing as one during the time of study.
• Evidence: The type of evidence for hybridization in the study system (genetic, phenotypic, etc.).
• Species: The species described in the paper. 
• OrganismType: The organism type described in the paper. 
• Nspecies: The number of species described in the paper. 
• Nind: The number of individuals described in the paper. 
• Nloci: The number of loci analyzed in the paper. 
• Locations: The number of sampling sites described in the paper. 
• Yearsofhyb: How long the hybridization has been ongoing for. 
• Markertype: Which type or types of genetic markers were used in the study. 
• Nhybridgen: How many generations of hybrids the paper noted to be present in the study system (F1, F2, etc.).
• Nbackcrossgen: How many generations of backcrosses the paper noted to be present in the study system.
• Anthropogenic: Whether the paper shows evidence for anthropogenic disturbance in the study system. 
• Introduced: Whether the paper shows evidence for species introduction in the study system. 
• Disturbance: Whether the paper shows evidence for non-anthropogenic disturbance in the study system. 
• DataAvailable: Whether the raw data for the paper has been made publicly available. 
• DataLink: Link to the raw data for the paper. 
• ContextSummary: A summary of the context surrounding the usage of the term "hybrid swarm" in the paper. 
• Notes: Notes on the paper by the reader. 
• Notes2: Additional notes on the paper by the reader or another author reviewing the paper/data. 

Code/software

For all data collection and analysis, we used R (version 4.1.2). Data collection was done using our hybrid_swarm_pubmed.R script and the R packages easyPubMed (version 2.13), remotes (version 2.4.0), litsearchr (version 1.0.0), and plyr (version 1.8.6). For plotting, we used our hybrid_swarm_plotting.R script, and R packages tidyverse (version 1.3.1), scales (version 1.2.1), patchwork (version 1.1.3), and ggsankey (no version). 

Access information

Other publicly accessible locations of the data:

• Github: https://github.com/amanda-meuser/Hybrid_Swarm_Paper