Generation of distancebased phylogenetic trees

Transcription

1 primer for practical phylogenetic data gathering. Uconn EEB Spring 2015 Session 12 Generation of distancebased phylogenetic trees Rafael Medina Yang Liu

2 confirmation BLST list Raw alignment Ref. alignment Generation of phylogenetic trees Specimen GenBank DN extraction Locus selection Primer design retrieval Bulk sequence upload mplification (PCR) ligner Refining PCR product cleaning Sanger sequencing Contig assembly ny troublesome sequence, potential contamination or relevant data that needs to be double-checked can take you back to the lab for confirmation Phylogenetic analysis (not in this seminar) Phylogenetic reconstruction

3 Some usual ways to infer a phylogenetic tree Distance methods Maximum Parsimony Maximum Likelihood Bayesian Inference Clustering of the sequences depending on the number of sites they differ Seeks for the tree(s) with the least number of changes Infers the tree(s) that makes most probable to observe the data (sequences) Provides the tree(s) with highest probability to be true assuming the data are correct

4 Some usual ways to infer a phylogenetic tree Distance methods Maximum Parsimony Maximum Likelihood Bayesian Inference They result in a single tree, but do not explore intensively the topological space They use powerful, heuristic methods to explore the topological space and will result in a high number of trees that can be synthesized in a consensus tree

5 Some usual ways to infer a phylogenetic tree Distance methods Maximum Parsimony They do not require any nucleotide substitution model to be used Maximum Likelihood Bayesian Inference They require the use of nucleotide substitution models

6 Some usual ways to infer a phylogenetic tree The details of phylogenetic inference under most of these methods lie out of the scope of this seminar, but we will learn how to make distance trees according two different distance methods: UPGM (Unweighted Pair-Group Method with rithmetic mean) NJ (Neighbor Joining)

7 UPGM: how to make a tree, step by step lignment

8 UPGM: how to make a tree, step by step lignment B C D E B 5 C 5 1 D E Distance matrix (number of mutations)

9 UPGM: how to make a tree, step by step lignment B C B C D E B 5 C 5 1 D E Distance matrix (number of mutations) Scale: 1.0 Find the shortest pairwise distance and make the first group. The length of the branches is half of this value

10 UPGM: how to make a tree, step by step B C D E B 5 C 5 1 D E B C BC 5 BC D E D 4.5 E 3.5 Make a reduced distance matrix using the mean values between each of the remaining taxa and the cluster BC Scale: 1.0

11 UPGM: how to make a tree, step by step B C D E B 5 C 5 1 D E B C BC 5 BC D E D E Make a reduced distance matrix using the mean values between each of the remaining taxa and the cluster BC (the rest remains without changes) Scale: 1.0

12 UPGM: how to make a tree, step by step BC 5 BC D E D E Repeat the first step with the reduced matrix B C D Scale: 1.0

13 UPGM: how to make a tree, step by step BC 5 BC D E D E Repeat the first step with the reduced matrix B C D D BC E D BC 4.75 E Scale: 1.0 nd so on

14 UPGM: how to make a tree, step by step BC 5 BC D E D E Repeat the first step with the reduced matrix E B C D D BC E D BC 4.75 E Scale: 1.0 nd so on

15 UPGM: how to make a tree, step by step 1.75 E BC D E 1.31 B BC 5 D E Repeat the first step with the reduced matrix = C D D BC E D BC 4.75 E D D BCE BCE Scale: 1.0 nd so on

16 UPGM: how to make a tree, step by step E B C D Scale: 1.0

17 Making trees using MEG6 Download MEG6 at (Free, versatile and intuitive) Once you run MEG you will see this window These menus will allow you to do different things with your data MEG uses its own alignment format, so the first thing you need to do is convert your fasta/nexus file into MEG The different datasets, sessions and trees will appear in the central area

18 Making trees using MEG6 Find your alignment and choose the input format and save it as a.meg file You will also see your alignment through the MEG text editor, but it is not very useful for us at this point and you can just close it

19 Making trees using MEG6 For our purposes we will not consider this sequence protein-coding region. This is the dataset you just loaded You can close it here The alignment can be opened in the MEG data explorer, which allows to fins easily relevant information in the alignment

20 Making trees using MEG6 Display invariant sites as dots Visualize: Conserved Variable Parsimony informative Singletons Highlighted nucleotides / total

21 Making trees using MEG6 The distance matrix will appear among the open items Distance matrix: Choose among different options in the yellow drop-menus

22 Making trees using MEG6 Generation of a tree: Setup parameters in the drop menus: Support test? Number of pseudoreplicates Pick the desired inference How the changes are considered? How gaps/missing data are considered?

23 Making trees using MEG6 Choose among different format styles Change the root, flip the nodes etc The new tree will appear among the open items Tree explorer window

24 Making trees using MEG6 Use the different tools to polish the displayed figure

25 Making trees using MEG6 Then export the Newick tree, or print as pdf