Table 1 A summary of the strength and weaknesses of the different approaches to reconstructing aquatic ecosystems and pheno- and genotypic variability over time in aquatic systems.
From: Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation
Method | Strengths | Weaknesses | References |
|---|---|---|---|
Palaeoecology based on fossil organisms | • >107 year time scales | • No genotype information | |
• Large datasets are available | • Labour intensive | ||
• Potentially quantitative | • Only some groups/species preserved | ||
Geochemical (bio)markers | • >107 year time scales | • No genotype information | |
• Large databases available | • Potential for porewater mobility | ||
• High throughput | • Lacks the taxonomic specificity of DNA sequences | ||
• Potentially quantitative | |||
Sedimentary eDNA timeseries | • So far, ~105 year time scales | • No direct phenotype information | See references in text |
• Cover all domains of life | • So far, above population level | ||
• High throughput | • Few reference sequences | ||
• Sequence data has the potential to link specifically to taxa or traits | • Potential for porewater mobility | ||
• Potentially quantitative (qPCR; so far only ~100 years) | • New bacterial and archaeal signals overprint the paleo-sequences, due to in situ growth | ||
• Risk of chimeras & contamination | |||
• Risk of bias in extraction | |||
Resurrection ecology | • So far, 101-102 time scales (much longer for Bacteria and Archaea) | • Labour intensive | See references in text |
• Linking genotype and phenotype directly | • Only some species preserved | ||
• Applicable at population level | • Potential bias in survivability, but single-cell approaches possible | ||
• Potentially quantitative |
