Taxonomic relationships between North American red oak species (Quercus section Lobatae) are not well resolved using genetic and morphological markers. Phenotypic plasticity, recent species divergence, and hybridization may all contribute to the unclear species boundaries in red oaks. We applied twenty-eight genomic and gene-based microsatellites, including outlier loci with potential roles in reproductive isolation and adaptive divergence between species, to natural populations of four monophyletic interfertile oak species: Quercus ellipsoidalis, Q. coccinea, Q. rubra, and Q. velutina. To better resolve the taxonomic relationships in this difficult clade, we assigned individual samples to species, identified hybrids and introgressive forms, and reconstructed phylogenetic relationships among the four species after exclusion of genetically intermediate individuals. Genetic assignment analyses identified four distinct species clusters, with Q. rubra most differentiated from the three other species. However, especially between Q. ellipsoidalis and Q. velutina, a comparatively large number of misclassified individuals (7.14%), hybrids (7.14%), and introgressive forms (18.83%) were detected. After the exclusion of genetically intermediate individuals, Q. ellipsoidalis grouped as sister species to the largely parapatric Q. coccinea with high bootstrap support (91%). Genetically intermediate forms in a mixed species stand were located proximate to both potential parental species, which supports recent hybridization of Q. velutina with both Q. ellipsoidalis and Q. rubra. Analyses of genome-wide patterns of interspecific differentiation can provide a better understanding of speciation processes and taxonomic relationships in this taxonomically difficult group of red oak species.

Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post-zygotic isolation mechanisms, such as ecologically dependent selection on adaptive loci, may therefore limit introgression. To test this hypothesis, we quantified hybridization and genetic divergence across the contact zone of four red oaks (Quercus section Lobatae) in the Great Lakes region of North America using a suite of 259 amplified fragment length polymorphisms and 27 genic and genomic microsatellite markers. First, we identified hybrids using genetic structure analysis and confirmed the reliability of our assignments via simulations. Then, we identified candidate loci for species maintenance with three complementary tests for selection and obtained partial gene sequences linked to an outlier locus and three other loci. We detected evidence of recent hybridization among all species and considerable gene flow between Q. ellipsoidalis and Q. velutina. Overall, c. 20% of Q. velutina had recent ancestry from Q. ellipsoidalis, whereas nearly 30% of Q. ellipsoidalis had a Q. velutina ancestor. Most loci were negligibly to weakly differentiated among species, but two gene-linked microsatellites deviated significantly from neutral expectations in multiple, complementary outlier tests. Both outlier loci were located in the same 15-cM bin on an existing Q. robur linkage map, a region under divergent selection in other oak species. Adaptive loci in this highly differentiated genomic region may contribute to ecological divergence among species and limit introgression. ADDITIONAL KEYWORDS: genetic divergence -introgression -outlier loci -Quercus sectionLobatae -red oaks -selective sweep.

• Premise of the study: Fourteen genomic microsatellite markers were developed and characterized in honey locust, Gleditsia triacanthos, using Illumina sequencing. Due to their high variability, these markers can be applied in analyses of genetic diversity and structure, and in mating system and gene flow studies.• Methods and Results: Thirty-six individuals from across the species range were included in a genetic diversity analysis and yielded three to 20 alleles per locus. Observed heterozygosity and expected heterozygosity ranged from 0.214 to 0.944 and from 0.400 to 0.934, respectively, with minimal occurrence of null alleles. Regular segregation of maternal alleles was observed at seven loci and moderate segregation distortion at four of 11 loci that were heterozygous in the seed parent.• Conclusions: Honey locust is an important agroforestry tree capable of very fast growth and tolerance of poor site conditions. This is the first report of genomic microsatellites for this species.

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To analyze the utility of isolated remnant populations for full-sibling (full-sib) identification among open-pollinated single-tree progeny in the outcrossing and insect-pollinated tree Gleditsia triacanthos L. (honey locust), we performed paternity analyses in forest fragments from two geographic regions using nuclear microsatellites. The first plot (Butternut Valley population) comprised only 7 trees, and 552 seedlings from a single seed parent were characterized at nuclear microsatellites. A large number of putative pollen donors (59) were identified in kinship analyses, but their individual contributions to the progeny were highly variable. Kinship and paternity analyses identified 149 putative full-sibs for genetic mapping sired by an external (unsampled) pollen parent. To better assess the frequency of long-distance pollen dispersal, a total of 180 seeds were collected from 6 seed parents in another fragmented population. In both plots, contemporary pollen dispersal occurred generally from outside the plots (99.38% and 87.50%–100% at the Butternut Valley and Ames Plantation sites, respectively) and thus over very long distances (>12 000 m in the Ames Plantation) suggesting that in highly fragmented landscapes, insect pollinators of honey locust are likely very effective long-distance dispersers.

Hypsipyla robusta Moore (Lepidoptera: Pyralidae), like many other moth species, shows selectivity when choosing host plants for its eggs. Four Meliaceae species (Khaya grandifoliola, K. ivorensis, Swietenia macrophyla, and Entandrophragma cylindricum) were established in a moist semideciduous forest in Ghana to study this selectivity at 12 and 21 months after planting. The analysis of variance (ANOVA) at a P -value of 0.05 was used to test the significance of differences in infestation by H. robusta between the species. H. robusta attacks were recorded by month 12 after planting in the field, and only Khaya spp. was attacked, with attacks evident on 15.5% of K grandifoliola and 6.6% K. ivorensis. Saplings in blocks closer to an older H. robusta infested K. grandifoliola stand had more infestation compared to saplings further away. The mean percentage of K. grandifoliola attacked was 38.9%, 38.9%, 13.3%, and 7.4% in 4 different plots located increasingly further away from the older infested plantation. A similar trend was found in K. ivorensis with 28.4%, 7.1%, 0.0%, and 0.0% in the plots located increasingly further away from the infested stand. These results indicate a higher number of shoot borer attacks at the edge of the plantation and in proximity to other infested plantations. After 21 months, the fastest-growing species and the fastest-growing individuals within the species were the most infested. K. grandifoliola recorded the fastest growth and most attacks followed by K. ivorensis and S. macrophylla. E. cylindricum recorded the least growth and no H. robusta infestation. After 21 months, the mean percentages of trees attacked were 59.1%, 23.7%, 5.6%, and 0.0% for K. grandifoliola, K. ivorensis, S. macrophylla, and E. cylindricum, respectively. Within species, the fastest-growing saplings experienced the most attacks. A positive correlation was observed between the plant size and H. robusta attacks (R2 = 0.76). Attacks resulted in the death of the apical shoot and the proliferation of multiple shoots in only the Khaya spp., with K. ivorensis recording a lower number of shoots than K. grandifoliola. These proliferated shoots were also attacked, and a positive correlation was observed between the number of proliferated shoots and H. robusta attacks (R2 = 0.84). These findings will assist plantation developers, forest managers, and investors in mahogany plantations to devise integrated pest management strategies to reduce the impact of Hypsipyla attacks on their plantations.