What can we learn about plant evolution from a robust phylogenetic framework?
<p>A robust molecular phylogeny provides insights into evolutionary history because it illustrates the order that different taxa have diverged from each other, and the changes that have accumulated between different taxa over evolutionary history. However, a molecular phylogeny does not provid...
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| Άλλοι συγγραφείς: | |
| Μορφή: | Thesis |
| Γλώσσα: | English |
| Έκδοση: |
2019
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| _version_ | 1826291735043506176 |
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| author | Carruthers, T |
| author2 | Scotland, R |
| author_facet | Scotland, R Carruthers, T |
| author_sort | Carruthers, T |
| collection | OXFORD |
| description | <p>A robust molecular phylogeny provides insights into evolutionary history because it illustrates the order that different taxa have diverged from each other, and the changes that have accumulated between different taxa over evolutionary history. However, a molecular phylogeny does not provide information about a range of other fundamental parameters in macroevolutionary research. This includes the absolute time-scale over which a clade has evolved, and the rate that different clades have diversified. In order to estimate absolute time-scales (referred to as divergence time estimation), and infer net diversification rates, speciation rates, and extinction rates (referred to as diversification parameter estimation), additional analyses are therefore required. As robust phylogenies are inferred for an increasing number of groups, and complex analyses are performed to infer macroevolutionary parameters in a greater variety of contexts, evaluating the robustness of methods for inferring divergence times and diversification parameters is more important than ever. Here, I evaluate the robustness of methods for inferring divergence times and diversification parameters. I show that even in the context of genomic scale datasets, among-branch-substitution-rate-variation that acts consistently across entire genomes causes considerable error in divergence time estimates, regardless of the quantity of molecular sequence data that is sampled. I then show that methods that implement multiple fossil calibrations with relaxed clock methods, which are designed to account for among-branch-substitution-rate-variation, make unrealistic assumptions about the fossil record. I show that these unrealistic assumptions are likely to be a further source of error in divergence time estimates. I then characterise the implications of these problems for estimating divergence times and diversification parameters within Ipomoea, and show that they can lead to very uncertain inferences. However, I show that if questions are carefully framed, and the assumptions of different methods fully accounted for, robust inferences can be made. This includes the inference that the storage root of the Sweet Potato (Ipomoea batatas) evolved in pre-human times, challenging the existing paradigm that it evolved relatively recently as a result of human domestication. It also includes the inference that there is a significant increase in net diversification rates for a clade of Neotropical Ipomoea that is of a scale equivalent to some of the most iconic radiations in the plant kingdom. Taken together, this thesis illustrates fundamental problems that underlie methods in macroevolutionary research, but highlights that when methods are used in the right context, they can serve as a basis for making novel and robust inferences about the natural world. </p>
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| first_indexed | 2024-03-07T03:03:53Z |
| format | Thesis |
| id | oxford-uuid:b1dd3e1b-1eb3-40f9-95bf-08e05e26ec65 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T03:03:53Z |
| publishDate | 2019 |
| record_format | dspace |
| spelling | oxford-uuid:b1dd3e1b-1eb3-40f9-95bf-08e05e26ec652022-03-27T04:07:17ZWhat can we learn about plant evolution from a robust phylogenetic framework?Thesishttp://purl.org/coar/resource_type/c_db06uuid:b1dd3e1b-1eb3-40f9-95bf-08e05e26ec65systematicsevolutionary biologybotanyEnglishHyrax Deposit2019Carruthers, TScotland, R<p>A robust molecular phylogeny provides insights into evolutionary history because it illustrates the order that different taxa have diverged from each other, and the changes that have accumulated between different taxa over evolutionary history. However, a molecular phylogeny does not provide information about a range of other fundamental parameters in macroevolutionary research. This includes the absolute time-scale over which a clade has evolved, and the rate that different clades have diversified. In order to estimate absolute time-scales (referred to as divergence time estimation), and infer net diversification rates, speciation rates, and extinction rates (referred to as diversification parameter estimation), additional analyses are therefore required. As robust phylogenies are inferred for an increasing number of groups, and complex analyses are performed to infer macroevolutionary parameters in a greater variety of contexts, evaluating the robustness of methods for inferring divergence times and diversification parameters is more important than ever. Here, I evaluate the robustness of methods for inferring divergence times and diversification parameters. I show that even in the context of genomic scale datasets, among-branch-substitution-rate-variation that acts consistently across entire genomes causes considerable error in divergence time estimates, regardless of the quantity of molecular sequence data that is sampled. I then show that methods that implement multiple fossil calibrations with relaxed clock methods, which are designed to account for among-branch-substitution-rate-variation, make unrealistic assumptions about the fossil record. I show that these unrealistic assumptions are likely to be a further source of error in divergence time estimates. I then characterise the implications of these problems for estimating divergence times and diversification parameters within Ipomoea, and show that they can lead to very uncertain inferences. However, I show that if questions are carefully framed, and the assumptions of different methods fully accounted for, robust inferences can be made. This includes the inference that the storage root of the Sweet Potato (Ipomoea batatas) evolved in pre-human times, challenging the existing paradigm that it evolved relatively recently as a result of human domestication. It also includes the inference that there is a significant increase in net diversification rates for a clade of Neotropical Ipomoea that is of a scale equivalent to some of the most iconic radiations in the plant kingdom. Taken together, this thesis illustrates fundamental problems that underlie methods in macroevolutionary research, but highlights that when methods are used in the right context, they can serve as a basis for making novel and robust inferences about the natural world. </p> |
| spellingShingle | systematics evolutionary biology botany Carruthers, T What can we learn about plant evolution from a robust phylogenetic framework? |
| title | What can we learn about plant evolution from a robust phylogenetic framework? |
| title_full | What can we learn about plant evolution from a robust phylogenetic framework? |
| title_fullStr | What can we learn about plant evolution from a robust phylogenetic framework? |
| title_full_unstemmed | What can we learn about plant evolution from a robust phylogenetic framework? |
| title_short | What can we learn about plant evolution from a robust phylogenetic framework? |
| title_sort | what can we learn about plant evolution from a robust phylogenetic framework |
| topic | systematics evolutionary biology botany |
| work_keys_str_mv | AT carrutherst whatcanwelearnaboutplantevolutionfromarobustphylogeneticframework |