Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to the northeastern United States. We present a chromosome-scale, haplotype-resolved genome of Q. rubra, a representative red oak species, generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Megabases (Mb) with 95.27% of the genome sequences scaffolded into 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Q. lobata and Q. mongolica reveal high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other oak and rosid tree species revealed that gene families associated with defense response were expanding and contracting simultaneously across the Q. rubra genome. Quercus rubra had the most CC-NBS-LRR and TIR-NBS-LRR resistance genes out of the nine species analyzed. Terpene synthase gene family comparisons further reveal tandem gene duplications in TPS-b subfamily, similar to Q. robur. Single major QTL regions were identified for vegetative bud break and marcescence which contain candidate genes for further research, including a putative ortholog of the circadian clock constituent cryptochrome (CRY2) and a family of eight tandemly duplicated genes for serine protease inhibitors, respectively. Genome-environment associations across natural populations identified candidate abiotic stress tolerance genes and predicted performance in a common garden. This high-quality red oak genome represents an essential resource to the oak genomics community which will further supplement the knowledge of Quercus genomics.

Animal seed dispersers may influence plant genetic diversity, though there are few examples linking disperser behavior to population genomic diversity. We hypothesized that breeding colonies of the frugivorous White-Crowned Pigeon (Patagioenas leucocephala) would increase population diversity and decrease population differentiation in fruit trees at nesting sites due to increased seed dispersal from foraging trips. We measured the density and extent of colonies at Parque Nacional Jaragua (Dominican Republic) and used nuclear and plastid SNPs from ddRADseq to examine the spatial genetic structure of two common species: poisonwood (Metopium toxiferum), a key fruit resource during the breeding season, and gumbo limbo (Bursera simaruba). We found that pigeon nesting aggregations in and around Parque Nacional Jaragua occupy areas between 3 and 5 Km2, with an estimated number of active nests for 2016 extrapolated to 3 km2 of 159,144  21,484 s.e., making this one of the largest breeding aggregations for the species across its range. However, colony locations did not determine tree genetic diversity and differentiation. Gumbo limbo (consumed by a diverse community) showed less isolation by distance than poisonwood. Saplings and plastid markers, expected to be more strongly influenced by seed dispersal, did not display geographic structure associated with colony sites, suggesting that patterns were not primarily due to pigeon foraging. Our results highlight the diversity of population genomic patterns among co-occurring species with similar ecological niches and demonstrate the limitations for frugivores to influence genetic differences among plant species.