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Whole genome bisulfite sequencing for bud, catkin and leaf of California Valley Oak, Quercus lobata (SW786)

ABSTRACT: WGBS sequencing of Valley Oak bud, catkin and leaf tissues

ORGANISM(S): Quercus lobata

PROVIDER: GSE174826 | GEO | 2021/05/22

REPOSITORIES: GEO

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Project description:Landscape characteristics and social behavior can affect the foraging patterns of seed-dependent animals. We examine the movement of acorns from valley oak (Quercus lobata) trees to granaries maintained by acorn woodpeckers (Melanerpes formicivorus) in two California oak savanna-woodlands differing in the distribution of Q. lobata within each site. In 2004, we sampled Q. lobata acorns from 16 granaries at Sedgwick Reserve in Santa Barbara County and 18 granaries at Hastings Reserve in Monterey County. Sedgwick has lower site-wide density of Q. lobata than Hastings as well as different frequencies of other Quercus species common to both sites. We found acorn woodpeckers foraged from fewer Q. lobata seed source trees (K(g) = 4.1 ± 0.5) at Sedgwick than at Hastings (K(g) = 7.6 ± 0.6) and from fewer effective seed sources (N(em)* = 2.00 and 5.78, respectively). The differences between sites are due to a greater number of incidental seed sources used per granary at Hastings than at Sedgwick. We also found very low levels of seed source sharing between adjacent granaries, indicating that territoriality is strong at both sites and that each social group forages on its own subset of trees. We discovered an interesting spatial pattern in the location of granaries. At Sedgwick, acorn woodpeckers situated their granaries within areas of higher-than-average tree density, while at Hastings, they placed them within areas of lower-than-average tree density, with the outcome that granaries at the two sites were located in areas of similar valley oak density. Our results illustrate that landscape characteristics might influence the number of trees visited by acorn woodpeckers and the locations of territories, while woodpecker social behavior, such as territoriality, shapes which trees are visited and whether they are shared with other social groups.

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Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus).

Project description:BACKGROUND:Hybridization and introgression are common phenomena among oak species. These processes can be beneficial by introducing favorable genetic variants across species (adaptive introgression). Given that drought is an important stress, impacting physiological and morphological variation and limiting distributions, our goal was to identify drought-related genes that might exhibit patterns of introgression influenced by natural selection. Using RNAseq, we sequenced whole transcriptomes of 24 individuals from three oaks in southern California: (Quercus engelmannii, Quercus berberidifolia, Quercus cornelius-mulleri) and identified genetic variants to estimate admixture rates of all variants and those in drought genes. RESULTS:We found 398,042 variants across all loci and 4352 variants in 139 drought candidate genes. STRUCTURE analysis of all variants revealed the majority of our samples were assignable to a single species, but with several highly admixed individuals. When using drought-associated variants, the same individuals exhibited less admixture and their allele frequencies were more polarized between Engelmann and scrub oaks than when using the total gene set. These findings are consistent with the hypothesis that selection may act differently on functional genes, such as drought-associated genes, and point to candidate genes that are suggestive of divergent selection among species maintaining adaptive differences. For example, the drought genes that showed the strongest bias against engelmannii-fixed oak variants in scrub oaks were related to sugar transporter, coumarate-coA ligases, glutathione S-conjugation, and stress response. CONCLUSION:This pilot study illustrates that whole transcriptomes of individuals will provide useful data for identifying functional genes that contribute to adaptive divergence among hybridizing species.

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