DOI: 10.5061/dryad.p5hqbzkmc
title: Population structure, landscape genomics, and genetic signatures of adaptation to exotic disease pressure in Cornus florida L. – insights from GWAS and GBS data

description: Understanding the consequences of exotic diseases on native forests is
 important to evolutionary ecology and conservation biology because exotic
 pathogens have drastically altered US eastern deciduous forests. Cornus
 florida L. (flowering dogwood tree) is one such species facing heavy
 mortality. Characterizing the genetic structure of C. florida populations
 and identifying the genetic signature of adaptation to dogwood anthracnose
 (an exotic pathogen responsible for high mortality) remains vital for
 conservation efforts. By integrating genetic data from
 genotype-by-sequencing (GBS) of 289 trees across the host species range
 and distribution of disease, we evaluated the spatial patterns of genetic
 variation and population genetic structure of C. florida and compared the
 pattern to the distribution of dogwood anthracnose. Using GWAS and
 gradient forest analysis, we identified genetic loci under selection and
 associated with ecological and diseased regions. The results revealed
 signals of weak genetic differentiation of three or more subgroups nested
 within two clusters—explaining up to 2-6% of genetic variation. The groups
 largely corresponded to the regions within and outside the eastern
 Hot-Continental ecoregion, which also overlapped with areas within and
 outside the main distribution of dogwood anthracnose. The fungal sequences
 contained in the GBS data of sampled trees bolstered visual records of
 disease at sampled locations and were congruent with the reported range of
 D. destructiva, suggesting fungal sequences within host genomic data were
 informative for detecting or predicting disease. The genetic diversity
 between populations at diseased vs. disease-free sites across the range of
 C. florida showed no significant difference. We identified 72 SNPs from 68
 loci putatively under selection, some of which exhibited abrupt turnover
 in allele frequencies along the borders of the Hot-Continental ecoregion
 and the range of dogwood anthracnose. One such candidate SNP was
 independently identified in two prior studies as a possible L-type
 lectin-domain containing receptor kinase. While diseased and disease-free
 areas do not significantly differ in genetic diversity, overall there are
 slight trends to indicate marginally smaller amounts of genetic diversity
 in disease-affected areas. Our results were congruent with previous
 studies that were based on a limited number of genetic markers in
 revealing high genetic variation and weak population structure in C.
 florida.
description: Population genetic datasets and sequences of GBS-tags per sample
 were exported as Fasta, Genepop, and PLINK files after processing GBS data
 via STACKS (version 1.35).
description: Various population genetic programs can process, analyze, or
 convert Genepop (.gen) or PLINK (.ped and .map) file formats, and
 sequences in Fasta (.fa) file may be searched against existing databases
 to find similar sequences and functional annotations. For aligning
 GBS-tags back to draft genomes of Cornus florida, Erysiphe pulchra, and
 Discula destructiva please contact original owners for latest version of
 draft genomes (see acknowledgement section of Pais et al. 2020).