In exercise 3 we inferred the phylogeny of extant bears and a timeline for their evolution using node dating. Node dating has several caveats, one which is that we hardly used any of the available fossil information. In this exercise we will explictly incorporate information from the fossil record into the diversification process i. The fossilized birth-death FBD process is a model that assumes extant samples and fossils were generated by the same underlying evolutionary process Stadler ; Heath et al.
Metrics details. Order Charadriiformes shorebirds is an ideal model group in which to study a wide range of behavioural, ecological and macroevolutionary processes across species. However, comparative studies depend on phylogeny to control for the effects of shared evolutionary history. Although numerous hypotheses have been presented for subsets of the Charadriiformes none to date include all recognised species.
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Phylogenetic trees are the result of most evolutionary analyses. They represent the evolutionary relationships among a set of species or, in molecular biology, a set of homologous sequences. The PhyloTree class is an extension of the base Tree object, providing a appropriate way to deal with phylogenetic trees. Thus, while leaves are considered to represent species or sequences from a given species genome , internal nodes are considered ancestral nodes. A direct consequence of this is, for instance, that every split in the tree will represent a speciation or duplication event.