DOI: 10.5061/dryad.xpnvx0ks0
title: Data from: Preserving wild pears: Using genomic data to assess species boundaries, interspecific hybridization, and genetic diversity to inform conservation

description: Wild congeners of cultivated fruit trees are vital sources of genetic
 diversity for crop improvement and key targets for conservation. However,
 cultivating crops within the range of rare wild congeners increases the
 risk of interspecific hybridization, threatening the genomic integrity of
 wild species. This is a concern for Pyrus in Central Asia, where a
 critically endangered wild species, P. korshinskyi, coexists with
 cultivated Pyrus communis and another widespread species, P.
 regelii, forming a species complex in which species boundaries
 are unclear, complicating conservation efforts. Here, we sought to assess:
 1) the distinctiveness of species, 2) the extent to which interspecific
 hybridization and introgression may reduce the genetic integrity of P.
 korshinskyi, and 3) genetic diversity and structure within P.
 korshinskyi.  Using RAD sequencing to genotype 185 individuals
 from 13 presumed wild and ex situ populations in Kyrgyzstan, we found that
 P. korshinskyi is genetically distinct, highly morphologically
 variable, but occasionally hybridizes with both P. regelii and P.
 communis. Morphometric analyses indicate that the parental species and
 hybrids can be differentiated based on leaf characters. Unexpectedly,
 several reportedly wild populations of P. korshinskyi were found
 to be clonally propagated; unfortunately, because Pyrus exhibits
 gametophytic self incompatibility and all of the trees are the same
 genotype, these propagated populations are mate limited, limiting their
 conservation value. While P. korshinskyi populations are genetically
 diverse, further efforts are needed to preserve wild genetic diversity ex
 situ. These findings guide conservation strategies to maintain genetic
 integrity and diversity of P. korshinskyi both in situ and ex situ,
 underscoring the importance of genetic analyses for conserving crop wild
 relatives, especially in complex cultivated-wild mosaics.
description: # Data from: Preserving wild pears: Using genomic data to assess species
 boundaries, interspecific hybridization, and genetic diversity to inform
 conservation
 [https://doi.org/10.5061/dryad.xpnvx0ks0](https://doi.org/10.5061/dryad.xpnvx0ks0) ## Description of the data and file structure Leaf tissue was collected and stored in silica for DNA extraction. Herbarium vouchers were deposited in the MO.  DNA was extracted using a modified CTAB method (Doyle and Doyle 1987). 2bRAD libraries were prepared following Wang et al. 2012 using dual index barcoded adapters to multiplex 96 samples per library. Samples were sequenced on an Illumina HiSeq 4000 using 1 × 50 bp reads. Two types of data are contained 1. .vcf genotype files generated from STACKS version 2.68 2. popmap files used to organize genotypes into populations for analyses. ### Files and variables #### File: stacks02_02_pyrus_popmap.txt **Description:** population map file used in stacks organizing individuals by species (113 individuals; see "unique dataset" in manuscript). #### File: stacks02_02_pyrus_popmap_ordered_E2W_new.txt **Description:** population map file used in for visualizing individuals in STRUCTURE, organizing the individuals by population form East to West (113 individuals; see "unique dataset" in manuscript). #### File: popmap_pops_kors_unique3.txt **Description:** population map file used in stacks organizing individuals of pyrus korshinsky by population (80 individuals). This represents a subset of the samples used in stacks02_02_pyrus_popmap.txt. #### File: populations.snps_korshinsky_only.vcf **Description:** genotypes for the pyrus korshinsky subset (80 individuals). #### File: populations.snps_unique_dataset.vcf **Description:** genotypes for the pyrus analyzed in this study (113 individuals; see "unique dataset" in manuscript) ## Access information Other publicly accessible locations of the data: * GenBank BioProject ID: PRJNA1224801 * [https://www.tropicos.org/](https://www.tropicos.org/) * [https://livingcollections.org/home](https://livingcollections.org/home)