Herbarium specimens are increasingly being used for molecular phylogenetics and evolutionary studies. However, due to DNA degradation over time, choosing the right genome for analysis is crucial.
Plastid genomes (plastomes) have been widely used due to their high copy number and conserved structure, making them easier to recover from degraded samples. However, nuclear genomes offer higher phylogenetic resolution and can capture hybridization and polyploidy, despite being harder to extract from historical specimens. Mitochondrial genomes, on the other hand, are less frequently used in plant phylogenetics due to their structural variability and lower mutation rates.
Given these factors, what do you think is the most suitable genome for herbarium-based phylogenetic studies? Have recent sequencing techniques such as Hyb-Seq, genome skimming, or RAD-seq improved the feasibility of using nuclear DNA from historical plant specimens?
I look forward to insights from researchers working with ancient DNA, herbariomics, and plant phylogenetics! Please share your experiences and recommended methodologies.
According to the Zeng et al. (2018) Plastid genomes are the most suitable for phylogenetic studies using herbarium specimens, especially in cases where DNA is highly degraded. Nuclear rDNA can complement these studies, particularly for species-level resolution and hybridization studies. However, low-copy nuclear genes remain a challenge and may not be reliably recovered from older herbarium samples.
Zeng, C.-X., Hollingsworth, P. M., Yang, J., He, Z.-S., Zhang, Z.-R., Li, D.-Z., & Yang, J.-B. (2018). Genome skimming herbarium specimens for DNA barcoding and phylogenomics. Plant Methods, 14(43). https://doi.org/10.1186/s13007-018-0300-0
I agree with the previous answer. Plastid genomes are the most suitable for herbarium specimens, and besides ezRAD-seq also helps to get the most out of them.
Hi, Dinusha,
Thank you for your excellent question! The plastid genome is indeed well-suited as a data basis for phylogenetic analysis. In comparison, the chloroplast genome is preferred for analysis due to its better stability and conservativeness.
Hope this helpful! Feel free to reacho out for more details.
Jelena Marinkov and Lucian Miles thank you very much for your valued inputs and explanations.
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