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MEDUSA Fails To Accurately Predict Rate Parameters of Large Clades
Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
2018 (English)Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
Abstract [en]

The methods of modelling diversity can be subject to multiple biases, give misleading results and at worst be wholly inaccurate. This work tests the limits of MEDUSA, a program commonly used to estimate diversification rates and assesses its effectiveness in doing so especially with regards to smaller or larger clades. MEDUSAs accuracy in calculating diversification rate (r) and the extinction rate () is, in many respects, determined by how well the program can account for biases inherent in phylogenetic modelling. Biases such as the large clade effect and the pull of the recent are well known in modelling and their respective impact can change depending on the size of the clades modelled. By testing MEDUSAs ability to model such clades it is possible to better understand the relationship between these biases and the clades sizes they appear to be most closely related to. To test MEDUSA, artificial clades were created using TreeSim (Stadler 2011A) with a set diversification rate (r) and the relative extinction () rate. These trees were then run through MEDUSA and assessed to see how close the estimates were from the original value input into the model. The models tested in MEDUSA were a fixed r model, a fixed speciation model and a fixed extinction model. Ultimately, and somewhat worryingly, this study finds that MEDUSA struggles to predict accurate overall diversification rates for both small and large clades, which occur more frequently than some may expect. These findings challenge our dependency on MEDUSA for predicting diversification rate, thus asks serious questions about what we perceive the true shape of speciation through time for clades considered out of ‘norm’ to be. 

Place, publisher, year, edition, pages
2018. , p. 40
Series
Examensarbete vid Institutionen för geovetenskaper, ISSN 1650-6553 ; 435
Keywords [en]
MEDUSA, birth-death models, diversity, phylogeny, large clades
National Category
Other Earth and Related Environmental Sciences
Identifiers
URN: urn:nbn:se:uu:diva-354604OAI: oai:DiVA.org:uu-354604DiVA, id: diva2:1221923
Subject / course
Earth science
Educational program
Master Programme in Earth Science
Presentation
2018-05-30, Norrland I, Geocentrum, Villavägen 16, Uppsala, 13:00 (English)
Examiners
Available from: 2018-06-20 Created: 2018-06-20 Last updated: 2018-06-20Bibliographically approved

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