In-class problems#
In-class Problems Week 6
Remember that for the in-class problems, you can use different resources (command line manual/help pages, browser-based searches, AI-based problem solving) to find an answer. There is no right or wrong approach to finding an answer to a problem.
Once a set of suitable orthologs has been identified, phylogenies can be inferred to address biological questions. In this exercise, you will explore the evolution of marine mammals.
Please upload the protein sequences of the tumor supressor gene p53 from several mammals, including many mammals you will be familiar with, to NGPhylogeny according to exercise 6.1. The protein sequences in FASTA format can be found at: /nfs/teaching/551-0132-00L/6_Phylogenetics/p53.marine.mammals.faa. A table that maps protein identifiers, common names and scientific names is provided here: /nfs/teaching/551-0132-00L/6_Phylogenetics/p53.meta.tsv.
The output tree can be exported to iTOL for visualization. Within iTOL, there is a useful feature to translate the protein identifiers into scientific species names. To do this, click on the “Advanced” tab on the control panel, click on “Assign taxonomy” and follow the instructions. Root the tree at its midpoint (Advanced->Other functions->Midpoint root).
Have mammals evolved to inhabit the marine environment once or on multiple occasions?
Are dolphins more closely related to cows or to elephants?
Are walrusses more closely related to dogs or pigs?
Are manatees more closely related to elephants or dolphins?
Further reading:
Convergent evolution of the genomes of marine mammals (note Figure 1).
There are two genomes, Pseudomonas aeruginosa /nfs/teaching/551-0132-00L/6_Phylogenetics/GCF_000006765.1_ASM676v1_genomic.fna and Prochlorococcus marinus /nfs/teaching/551-0132-00L/6_Phylogenetics/GCF_000007925.1_ASM792v1_genomic.fna, that we want to compare in terms of their occurence and life style. With this in mind, consider the following questions:
What is their biogeographic distribution?
What types of samples do they occur in and can we in turn infer something about their lifestyle?
Note: There will be no example solutions for in-class problems. It is expected that students take notes and engage in the discussions during the lecture. If questions come up, students can use the Slack channels to receive help.