My nuclear and cpDNA are incongruent, and We keep them separate. I would like to do biogeography analyses. Which kid of trees, nuclear or cpDNA, are prefered for this analysis and why?
Hello Maryam,
in phylogenetic analyses, both nuclear and cpDNA markers can be used and the results compared. Chloroplast markers generally have less polymorphism and are more suitable for comparing populations or species to each other, whereas nuclear markers are more variable and easier to capture variation within populations. As for chloroplasts, they are inherited in a single lineage (there is no recombination as with nuclear DNA), so it genetic information is inherited in a nearly constant way from one generation to the next, which may make it easier to know exactly how the different lineages separated.
HelloLukasz,
Thanks for your response. You'r right. But when it comes to hybridization, we possibly have a different story. The cloroplastic genum cannot depict the exact inheritances. At this point, how can we evaluate which ones, cloroplastic or nuclear markers, are better?
To know the exact inheritances, it is best to use both nuclear and plastid data. However, using chloroplasts can give good insight into past episodes of hybridization, e.g:
Tian, X., Shi, L., Guo, J., Fu, L., Du, P., Huang, B., ... & Wang, Z. (2021). Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts. Frontiers in plant science, 12, 804568-804568.
https://www.researchgate.net/publication/357156493_Chloroplast_Phylogenomic_Analyses_Reveal_a_Maternal_Hybridization_Event_Leading_to_the_Formation_of_Cultivated_Peanuts
If we are interested in variability between species or isolated populations, the less variable chloroplast markers seem to be a better choice.
- Badges
- Science topic
- Similar topics
- Linguistics
- Composition Studies
- Writing