The 27-meter-high tree died last year after its roots rotted from exposure to seawater, but it has been hollowed out and filled with carbon fiber and adorned with replicated branches and leaves.
Sampling followed a Before-After, Control-Impact design, with replicated samples being collected at one control site and two treatment sites, both before harvesting and then again seven to eight years after the harvest that established the WHS.
Current common practice for dealing with replicated data is to average each subject replicate sample set, reducing the dataset size and incurring loss of information.
In the 2003 environments, the inbreds and hybrids were grown separately in adjacent blocks, with replicated B73 plots within each block.
In this way, a two-factor design is created, with replicated manipulations.
Therefore, in the analysis of variance, we estimated best linear unbiased estimates (BLUEs) separately for the two environments with replicated data.
The third option combines the two former ones, with replicated genotyping only for samples where three or fewer mismatches at different loci were observed.
Communities of dependent species associating themselves with replicated genotypes across these sites could then be analysed to robustly estimate the effects of both foundation species genotype and environmental contrasts.
Knapp and Bridges (1990) analyzed the expected mean squares of a model describing the sources of variation included in a QTL mapping experiment with replicated progenies and calculated power of QTL detection for different resource allocation strategies, not considering the cost of genotyping.
We compared our data with replicated candidate-gene studies, which were derived from (19), as well as the recent GWA reports that implicated intergenic intervals at the 5p14.1 CDH9– CDH10 and 5p15.2 SEMA5A– TAS2R1 loci, respectively (20, 21, 24) (Supplementary Material, Tables S5 and S6).
