To explore whether allele frequencies of the EuroAIMs differed significantly among the Spanish samples, we treated each individual EuroAIM marker as a candidate locus for association in a mock study where Canary Islanders were taken as "cases" and Iberians were considered "controls".
To simulate partially digested samples we treated the earthworm pieces with bleach.
To evaluate the effectiveness of catalase in destroying H2O2 in samples, we treated some samples from the mixed standard (pH 3.2) + H2O2 control experiment (10 mL) with 20 μL of a 1% catalase solution.
Furthermore, to neutralize the soluble fraction of endotoxin associated with the PM samples, we treated added Polymyxin B (PMB), an antibiotic that specifically binds LPS and prevents its binding to TLR4 receptors on the macrophages.
Because the iControl has more than 3000 samples, we treat it as a background population for our TCGA analysis and use it as a control group (that is also used in AGS).
The root of M2b in our tree differs in two positions to the earlier definition of Sun et al. [ 7] i.e. transition at np 182 is present in all of our M2b samples so we treated this as basal mutation and lack of this in one sample of Sun et al. [ 7] could be better explained by reversion event, second our all M2b samples has poly 'A' at np 16180 16182 and twelve 'C's thereafter.
The replication analysis was performed using the Geuvadis DNA-seq samples where we treated each Geuvadis population separately in a meta-analysis.
According to the AQS ambient pollutant manual (U.S. EPA 2004), daily observations can be estimated in terms of the arithmetic mean of hourly observations only if the number of these observations is greater than 18 (i.e., ≥ 75% of intended samples); otherwise, we treated them as missing data.
To enrich for plasmid DNA in the sample, we also treated with Exonuclease V (NEB) to degrade linear DNA fragments.
Based on this information, and our sample of Araliaceae, we treated this fossil as the first fossil evidence for the most inclusive clade that excludes Aralia and Panax.
