Preserving wild pears: Using genomic data to assess species boundaries, interspecific hybridization, and genetic diversity to inform conservation

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&n..., , , # 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 i...,