As biotechnology improves, we know more and more about plant genetics and evolutionary relationships. We can use the tools available to resolve evolutionary relationships between plants, at least theoretically. In practice, plant evolutionary research can be really challenging. Plants are notoriously promiscuous—many plants can hybridize, and others will spontaneously double all their chromosomes and become a new species. This makes it tough to know who is most closely related to whom.
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When scientists want to know how two plants are related, they have a few choices. They can look at the morphology of the plant, compare it to other species, and conclude that species that look the same must be closely related. This is how plant classification used to be done. But if you know a little about evolution, you know that species living in the same habitat tend to share traits and look alike because of convergent evolution. Luckily, now we have technology on our side.
Evolutionary biologists use phylogenetics to study how species are related to each other. Phylogenetics is the study of the evolutionary history of a group of organisms using genetic information. Scientists look at the DNA sequences of organisms and compare them to see how different they are. The more similar a DNA sequence, the more closely related two organisms are.
Phylogenetics uses phylogenetic trees, also called phylogenies to show how different species or genera or families are related. These are similar in concept and look to a family tree you might use to describe the relationships between your relatives.
Every so often, a group of scientists called the Angiosperm Phylogeny Group revises the phylogenetic tree for the flowering plants based on new studies that have been done. For more information on current plant classifications, see the Angiosperm Phylogeny website or the wikipedia page about the APG.