Table 1 Measures and assays for the factors that go into the Evo- and Eco-indices

Diversity (D)

• Divergence^12,13,14,46

• Number of clones (richness)^6,12,13,14

• Shannon index^12,13,14

• Simpson's index^12,13

• Functional diversity^115,169,170

• Phylogenetic trees^20,61,62,63

• Whole-exome and whole-genome sequencing

• Multi-region sequencing

• SNP arrays

• Methylation arrays

• FISH

• Single-cell DNA and RNA sequencing

• Cell-free DNA sequencing¹⁹

• RNA-Seq

• Proteomics

• Radiology

Change over time (Δ)

• Mutation rates^17,178

• Estimates of selection^17,179

• Clonal expansion rates¹⁴

• F_ST (Ref. 60)

• Nei's standard genetic distance^57,58

• Change in above diversity statistics

• Longitudinal sampling

• Whole-exome and whole-genome sequencing

• Cell-free DNA analysis¹⁹

Hazards (H)

• Abundance of infiltrating lymphocytes^82,83

• Morisita–Horn index of colocalization of cancer cells and lymphocytes⁷⁵

• Signatures of immune activation^82,83,101

• Density of pathogenic microorganisms⁹⁹

• Prevalence of microbial virulence genes¹⁰⁵

• Automated image analysis

• Immunohistochemistry

• RNA-Seq

• 16S rRNA sequencing

Resources (R)

• Degree of hypoxia^146,149

• Density of blood vessels^147,148

• Colocalization of cancer cells with fibroblasts¹⁶⁰

• Concentration of ATP¹⁵¹, glucose and other nutrients

• Blood flow^152,154

• Automated image analysis

• Immunohistochemistry

• MRI or PET–CT scans

• Intravenous induction of EF5

• Luciferase luminescence

• Mass spectrometry