DOI: 10.5061/dryad.1g1jwsv6r
title: Suturing fragmented landscapes: Mosaic hybrid zones in plants may facilitate landscape restoration

description: Many widespread plant taxa of western North America have diversified into
 phenotypically and genetically divergent lineages due to complex
 biogeographic histories across heterogeneous landscapes. Mosaic hybrid
 zones can form when geographically co-occurring yet environmentally
 distinct lineages cross-pollinate and form hybrids that occupy unique
 environmental niches absent of a geographic cline. This expands the total
 environmental space across which parental and hybrid individuals grow,
 resulting in larger, less fragmented geographic distributions. Here, we
 highlight hybridization mosaics across three study systems containing taxa
 critical to widespread plant communities in western North America:
 Ericameria nauseosa, Artemisia tridentata, and Sphaeralcea fendleri. The
 systems contain diverged taxa that co-occur geographically across the
 landscape, though not environmentally, and hybridize readily.
 Hybridization among taxa has facilitated niche expansion into intermediate
 environments consistent with unique combinations of adaptive genetic
 variation, creating more continuity within each study system (study
 systems occupy ~820–270,000 km2 more geographic space by virtue of
 hybridization). Furthermore, hybrids are predicted to play important roles
 in future climates (they occupy 8–475% more geographic area compared to
 present in a high emission climate scenario). This convergent pattern
 signals mosaic hybridization as an underappreciated mechanism with broad
 ecological and evolutionary ramifications and suggests understanding the
 consequences of this process may be critical to predict responses of taxa
 to changing climates. Moreover, leveraging mosaic hybridization may assist
 the creation of restoration management plans that aim to mitigate the
 deleterious effects of habitat fragmentation on ecosystems in the context
 of climate change.
description: # Suturing fragmented landscapes: Mosaic hybrid zones in plants may
 facilitate landscape restoration
 [https://doi.org/10.5061/dryad.1g1jwsv6r](https://doi.org/10.5061/dryad.1g1jwsv6r) ## Description of the data and file structure Directories are associated with each of the three taxa.  R_files:  * Rmd for analyses for each of the three taxa * Imports.R file with custom R functions * Rmd for final figure generation for main text and SI Genotype: * Filtered VCF file * genotype probability file from Entropy * Pop_*ID* is the individual IDs, lineage assignment, ancestry coefficients, and PC axes in the same order as the filtered vcf file and the genotype probability file ### Files and variables ### Folder: R\_files #### File: Imports.R **Description:** Custom R functions to be called by other R scripts #### File: hybrid\_figures.R **Description:** R file to make figures for the main text  #### File: hybrid\_figures\_SI.R **Description:** R file to make figures for the SI text. #### File: ARTR\_hybrid.R **Description:** All analyses for *Artemisia tridentata* datasets. #### File: ERNA\_hybrid.R **Description:** All analyses for *Ericameria nauseosa* datasets. #### File: Sph\_hybrid.R **Description:** All analyses for *Sphaeralcea species* datasets. ### Folder(s): *A. tridentata, E. nauseosa, Sphaeralcea* **Description:** Each folder contains the same files in the same format for each taxa.  #### File: XXX.vcf.gz **Description:** Filtered VCF file #### File: gprobAll.txt **Description:** Genotype probability file created with Entropy (rows = indv, columns = loci) #### File: Pop\_ID.csv **Description:** Population ID file with rows in the same order as the vcf and gprob file ##### Variables * Sp: Species * Pop: Population * Sp_Pop: 'Species_Population' * ID: Individual * All: Full population name 'Species_Pop_ID' * long: Longitude * lat: Latitude * A1/A3: Ancestry coefficients as estimated by entropy  * Sp_Anc: Species and estimated ancestral classification (parental species or hybrid) * Anc: Estimated ancestral classification (parental species or hybrid) * Label2 (for *Sph* only): Estimated ancestral classification (S. fendleri, Other Sph species, or hybrid) * PC1: PC1 * PC2: PC2 * PC3: PC3 * PC4: PC4 * PC5: PC5 ## Code/software | | ***E. nauseosa*** | ***A. tridentata*** | ***Sphaeralcea***\*\* sp.\*\* | | :----------------------------------- | :---------------------- | :---------------------- | :------------------------------ | | **Reduced representation libraries** | ddRADseq | ddRADseq | ddRADseq | | **restriction enzymes** | EcoRI & MseI | EcoRI & MseI | EcoRI & MspI | | **Pippin prep size selection** | 350-450bp | 350-450bp | 400-600bp | | **sequencing type** | single-end | single-end | single-end | | **sequencing platform** | Illumina HiSeq 4000 | Illumina NovaSeq 6000 | Illumina NovaSeq 6000 | | **sequencing facility** | University of Wisconsin | UTGSAF | University of Oregon | | **decontamination /** | github.com/ncgr/tapioca | github.com/ncgr/tapioca | \*process\_radtags \*(STACKS) | | **demultiplexing** | custom Perl script | custom Perl script | \*fastq-multx \*(Aronesty 2011) | | **avg. reads per indv.** | 2276267 | 2276703 | 1872931 | | **reference assembly** | *de novo* | genome | *de novo* | | **reference assembly method** | cd-hit-est v4.8.1 | Melton \*et al., \*2022 | STACKS v2.6 | | **alignment method** | bwa-mem v0.7.17 | bwa-mem v0.7.17 | STACKS v2.6 | | **variant calling method** | bcftools v1.9 | bcftools v1.9 | STACKS v2.6 | | **num. of indv.** | 600 | 407 | 366 | | **num. of loci** | 1613057 | 2766918 | 88140 | | **filtering method** | vcftools v0.1.16 | vcftools v0.1.16 | vcftools v0.1.16 | | **minor allele freq. (MAF)** | 0.02 | 0.01 | 0.02 | | **max. missing data (loci)** | 30% | 40% | 40% | | **thinned** | 100bp | 100bp | 100bp | | **max. missing data (indv.)** | 40% | 50% | 50% | | **min. mean read depth** | 3 | 2 | 10 | | **max. mean read depth** | 25 | 25 | 50 | | **min. quality** | 750 | 100 | 999 | | **min. Fis** | -0.5 | -0.5 | -0.5 | | **final mean** | 7.25x | 3.18x | 24.69x | | **final num. of indv.** | 586 | 397 | 366 | | **final num. of loci** | 22917 | 13003 | 7271 | ## Access information **Access information** Other publicly accessible locations of the data: * For E. nauseosa:  * [https://datadryad.org/stash/dataset/doi:10.5061/dryad.j0zpc86f4](https://datadryad.org/stash/dataset/doi:10.5061/dryad.j0zpc86f4) * [https://doi.org/10.1093/evolut/qpad207](https://doi.org/10.1093/evolut/qpad207)