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Pros and cons of phylogenetic reconstruction methods and how these methods have been used to reconstruct the evolutionary history of mammals

Pros and cons of phylogenetic reconstruction methods and how these methods have been used to reconstruct the evolutionary history of mammals

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An essay for the 2011 Undergraduate Awards (Ireland) Competition by Megan McKerchar. Originally submitted for DN008 at University College Dublin, with lecturer Dr. Emma Teeling in the category of Life Sciences
An essay for the 2011 Undergraduate Awards (Ireland) Competition by Megan McKerchar. Originally submitted for DN008 at University College Dublin, with lecturer Dr. Emma Teeling in the category of Life Sciences

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Published by: Undergraduate Awards on Aug 31, 2012
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10/27/2013

 
Megan McKerchar 
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06375022
Pros and cons of phylogenetic reconstruction methods and how these methods havebeen used to reconstruct the evolutionary history of mammalsIntroduction
Molecular data and their use to infer evolutionary history are become more and moreaccessible due to better knowledge and cheaper methods. More molecular data ispublished in modern papers than all the molecular data in the 20
th
century combined(Asher 
et al 
, 2009). Optimality criterions are widely used in assessing differentphylogenetic tree hypothesizes (Lartillot & Philippe, 2004). Broadly, criterions comparealternative phylogenies by scoring them and then use algorithms to put a value on thetree which defines the “best” tree from the data available (Swofford
et al 
, 1996). Thisranking of alternative trees helps to demonstrate how well the tree is supported. Purelyalgorithmic methods can be used to infer phylogenetic relationships but, unlikeoptimality criterion they don’t look at all of tree space only the specific tree given.However each criterion method has different evolutionary assumptions and as such hasdistinct advantages and disadvantages which directly affect the resulting hypothesis.When producing a tree these advantages and disadvantages need to be carefullyweighed before and after using the criterions that defined the tree. This essay willdiscuss these assumptions, how they affected the resulting tree with references to thecurrent mammal phylogeny.
Maximum Parsimony (MP)
This theory is based on Occam’s razor; it uses the idea that the simplest explanation isthe correct answer where the minimum number of changes is used to infer the tree. Itwas one of the first methods used to calculate phylogenetic trees (Felsenstein, 2004)and possibly one of the simpler methods still in use today. MP uses a post-order traversal which defines the minimum number of required character state changes by asingle pass over the tree (Swofford
et al 
, 1996). The advantage of this method is it’srelatively quick and easy to calculate as no model is required.
 
Megan McKerchar 
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06375022Maximum parsimony assumptions are ambiguous relative to other optimality criterionsand therefore it’s more difficult to assess the power of maximum parsimony (Lartillot &Philippe, 2004). This is because assumptions of MP are not explicit and largely implicitbecause no precise model is used, however evolutionary processes are still assumed(Swofford
et al 
, 1996). At the very minimum MP assumes that evolutionary processeswhich could have lengthened the branch length have not occurred. Also MP only usesinformative sites, therefore any sites with the same character are ignored as they areuninformative and according to parsimony tell us nothing. Therefore not only does MPloose information, it can’t account for unobserved substitutions or superimposedchanges; however this can be corrected for by using a Hadamard conjugation. This datatransformation can create an entirely new matrix (Swofford
et al 
, 1996).Other more defined parsimony methods have different assumptions like Fitch andWagner parsimony assumes free reversibility and equal probability of changes such astransitions and transversions are equally likely. Therefore the tree can be rooted at anypoint and have no change in branch length as the ancestral condition is not considered.Simply put as long as the tree is the shortest length possible the criterion has beensatisfied. Dollo parsimony does not make the assumption of symmetrical probability of character changes and therefore it can use ancestral conditions from an outgroup taxato infer changes up the tree. This method is good for restriction site data. Transversionparsimony uses weights for transitions than transversions to calculate the likely hood of certain steps occurring.This method needs to be used with care as do all methods when it comes tohomoplasy. Such an example of where homoplasy can lead to the wrong phylogenetictree, is shown by Pettigrew
et al 
(1989). Megabats and primates were placed together from extensive morphological features where 29 of 33 features agreed betweenmegabats and primates and only one feature agrees with microbats. Many of thesefeatures are in reference to the vision and visual brain pathways. In hind sight we areable to see that these features are convergent because primates and megabats both
 
Megan McKerchar 
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06375022rely on an acute visual system for orientation, feeding and surviving. Therefore these 29features are homoplastic because both groups need them for the same purpose/function, i.e. analogous.
Maximum Likelihood (ML)
ML methods consistently outperform distance methods and MP by being the mostasymptotic consistency (Lartillot & Philippe, 2004), meaning that the method willapproach a constant (the asymptote) continuously and therefore is reliable. Consistencywas proposed by Felsenstein and is the ability to continually arrive at the same value asmore data is added. However ML does require heavy calculations due to comparison of numerous alternative hypotheses (Swofford
et al 
, 1996).Various different models exist that vary in the number of different substitution typesincorporated. As a result ML methods are highly dependent on the model they use, if the model is wrong the results could be wrong. This is not to say that a perfect model isrequired, a good result can come from a good model provided it uses the mostimportant evolutionary parameters involved for that sequence (Swofford
et al 
, 1996).But this requires knowing what type of model to use and what evolutionary parametersare important. For example is a simple Juke Cantor model good enough to explainnucleotide substitution or is the more complex GTR (general time reversible model)required. The choice of the ‘right’ model requires a goodness of fit χ
2
statistic whichcompares observed data with expected from model prediction. It’s important to use amodel that fits the data and that isn’t just comparably better than other models(Swofford
et al 
, 1996).The models are based on a Markov chain and as a consequence one of theassumptions is that the nucleotide sites evolve independently at the same rate. This cancause an underestimation of the number of multiple changes and similar to MP can bepositively misleading. However this can be corrected for by adding a new relative rate

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