What are the advantages and disadvantages of using DNA sequence data for assessing relationships between the major groups of land plants?
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Plants What are the advantages and disadvantages of using DNA sequence data for assessing relationships between the major groups of land plants? The relationships between land plants, particularly the lower levels of the Bryophytes and the origins of the Angiosperms, has been a highly contested debate throughout the history of plant sciences. The introduction of molecular analysis of the relationships between these major groups, in the form of DNA sequence data, has revolutionised the subject in the last twenty years. It has affected the key aspects of plant phylogeny. Robust and unequivocal interactions have been identified confirming the phylogenetic tree, although it's intricacies and temporal detail is still far from complete. Although it may seem that DNA sequence data is the answer to these problems there are still things that require morphological evidence, a practice that is as old as plant sciences itself. This essay will outline the contributions made by DNA sequencing data to plant phylogeny and its limitations. The taxonomy of the land plants and subsequent theories of their evolution has been investigated for the past two centuries, however the contributions of Linnaeus in 1753 laid a sound foundation for future study of the subject. Morphological data has been accumulating steadily for the past 250 years, but for the first 100 it mainly concerned the question of taxonomy.
that lineage of plants and there is very little statistical probability that an exactly comparable character could of arose independently in another lineage, even in 5S rRNA the chances of an exact match are 4120 and even if an exact match is not required the numbers are still astronomical. Another advantage of the heritable traits of DNA is that specific markers exist which are common to all plants, the characters are not reliant on being expressed in the phenotype, which allows for analysis across families and of loss of function (the gene will still be present but inactivated). There are however problems regarding the collection of DNA sequence data. The main problem is that DNA at the moment can only be obtained from extant species; the implications of this will be discussed later. Obtaining ancient DNA from fossilised tissue is very difficult and prone to experimental contamination. 1990 was the first occurrence of ancient DNA sequence data (Goldberg et al) obtained from plant fossils 15-20 MYA. Although sequences had been identified the microscopic amounts of DNA were subject to PCR product contamination and the results were disputed. Smith  created these guidelines for the acceptance of ancient DNA data; 1. Amplification products should make sense.
Fossil data based on morphological analysis provides the answer to many of these problems. Fossils provide direct evidence for the rapid divergence and mass extinction processes, allowing absolute temporal calibration of the molecular clock. They also provide information that can be used to "fill in the gaps" where DNA sequence data fails to concerning the branching of the tree if outgrouping is unsuccessful, resolving conflicts at the nodes. This allows for the correct rooting of groups, removing long branch attrition artefacts that have to be based on extant species. The ability to analyse extinct species provides key information regarding the topology of the tree constructed and larger data sets across more taxa leading to a more detailed tree. Conclusions DNA sequence data has not removed the need for morphological assessment of the relationships between land plants, but it has provided a new route of analysis which provides much higher resolution and statistically robust data from which new hypothesis can be drawn from. It is reassuring to know that molecular analysis has not upset the overall topology of the tree, in fact it has re-affirmed conclusions regarding groups and families drawn up on morphological characters. Although morphology is limited in its robustness it does provide the key framework to which all DNA sequence analysis is hung from and the data obtained serves to augment and refine the work already provided by 300 years of study.
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