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Can you teach me how to read the phylogenetic tree??

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thanks a lot

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Thank you very much.

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We keep them and proceed with the tree construction

I believe that negative FST values can be considered as 0's

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Hello Sufyan, To save the alignment in fasta format, please follow the following Data- Export alignment - fasta format. Or you could Print the screen after selecting the region containing alignment and colours and size of the window. Or you could perform the multiple sequence alignment using muscle in the following web tool www.ebi.ac.uk/Tools/msa/muscle/

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The "Original Tree" provides confidence levels for each clade. While the "Bootstrap Consensus Tree" collapses the weakest clades. But, i would recommend to construct the tree using other methods like Mamimum likelihood etc to check the reliability of your phylogenetic tree and use the original tree.

@@BiologyLectures thankyou very much!!

@@BiologyLectures What do you mean by that, especially when u said that the consensus tree collapses the weakest clades? Is that mean that the consensus tree is the one more optimized tree? Thank you in advance!

Unfortunately, you will have to provide the required number of samples. One suggestion, you can repeat one sample just to fulfill the requirement.

For the sequences and data subset options selected, MEGA found zero common sites. If you selected the complete deletion option then you might achieve better results using the pairwise deletion option, as complete deletion removes all sites containing a gap in any part of the alignment. If you selected the pairwise deletion option then MEGA was unable to calculate the distance between one and several of the sequence pairs in the alignment. To identify such pairs compute a pairwise distance matrix using the p-distance method and look for the word “n/c” in place of the pairwise distance value.

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Hi You could try to zoom the screen to the maximum and then do the screenshot.

You can type in the name of the gene ids or accession number in the search bar.

@@BiologyLectures Yes sir, I know that. But what exactly is the gene ID for the sequences shown in this video?

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As described in the video, First obtain the nucleotide sequences for all the genes, and please choose DNA sequences while performing sequence alignment and do exactly how it has been described in the video. Thank you

@samugoku10 You can get protein sequeces from this portal: www.uniprot.org/

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Please use NCBI database

Whichever the sequence you use, please provide accesion number of it in your methods. Ideally use the sequence with close 100 percent or close to 100 percent identity.

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Most welcome

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Yes, we can.

We did Ctrl+C and Ctrl+V. Please restart the computer and the program and follow the exact steps we followed . Hope this helps.

@@BiologyLectures Thanks for the reply. No couldn't paste even after several trials. Then another video helped to do so. We should convert the text file to fasta file and then we could upload the file rather copy and paste. This info for those who had similar issue in copy & paste method.

@@tungalasuresh6248 hi, how do you convert the text file to a fasta file?

@@melissajoyabrahams9976 Hi it's simple. after saving in txt file. Rename the file to .fasta that's it.

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@@BiologyLectures thank you. So my question is if the topology show 2 big clades and one clade contains 10 species show paraphyletic and its on repetition. Like 1 commom ancestor has 2 descendants A and B. Then B has 2 descendants C and D, then D has 2 descendants E and F, and it kept happen. How should i explain this on the result of the report? Is it paraphyletic relationship?

@@sunflowers5990 Based on the scenario you described, where the phylogenetic analysis shows two big clades and one of them contains a repeated pattern of branching, it is likely that this clade exhibits a paraphyletic relationship. A paraphyletic group is a group of organisms that includes a common ancestor and some, but not all, of its descendants. In your case, the clade with the repeated pattern of branching represents a paraphyletic group because it contains the common ancestor (originating from the root of the tree) and only a subset of its descendants. To explain this in the report, you can mention the following points: Describe the phylogenetic analysis: Provide a brief overview of the methodology used for constructing the phylogenetic tree, such as the type of molecular data or morphological characters analyzed, and the specific method of tree reconstruction employed (e.g., maximum likelihood, Bayesian inference, neighbor-joining, etc.). Present the overall topology: Summarize the general structure of the phylogenetic tree and mention the presence of two major clades. Highlight the repeated branching pattern: Specify the clade that exhibits the repeated pattern of branching, where one common ancestor gives rise to two descendants, and subsequent descendants continue to split into two lineages. Identify the paraphyletic relationship: Explain that this repeated branching pattern indicates a paraphyletic relationship within the clade. Emphasize that a paraphyletic group includes the common ancestor and only some of its descendants, excluding others. Discuss the possible reasons: Offer possible explanations for the observed paraphyletic relationship, such as incomplete lineage sampling, hybridization events, or evolutionary processes that led to extinction or exclusion of certain lineages from the clade. Highlight the significance: Discuss the implications of the paraphyletic relationship in the context of evolutionary biology and phylogenetic analysis, considering the potential impact on our understanding of evolutionary relationships and the need for further investigation or data to resolve the relationships more accurately.

@@BiologyLectures what a neat explanation, i appreciate it a lot 🙏🏻 thank you so much! I have another question, i still dont get whats the essential difference between sister taxa/sister clade to monophyletic clade?

@@sunflowers5990 You are most welcome. Sister taxa or sister clades refer to two or more taxa or clades that are each other's closest relatives within a larger group. In other words, they share a common ancestor that is exclusive to them. Sister taxa can be thought of as siblings in a family tree, where they share a parent but are not necessarily part of the same larger group. On the other hand, a monophyletic clade (also known as a monophyletic group or a clade) is a group of organisms that includes an ancestor and all of its descendants. A monophyletic clade represents a complete lineage within a phylogenetic tree and is defined by a single common ancestor and all of its evolutionary descendants. This means that all the members of a monophyletic clade share a more recent common ancestor with each other than with any organisms outside of that clade. To illustrate the difference, imagine a phylogenetic tree with several branches representing different taxa or clades. If two branches emerge from a common node and have no other branches originating between them, those two branches would be considered sister taxa or sister clades. They are close relatives but may not share the same larger group or lineage. On the other hand, if a group of branches emerge from a common node and include all the descendants of that node, forming a complete lineage, that would be a monophyletic clade. It represents a distinct group that shares a common evolutionary history.

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It does matter. And to fix this problem, we would recommend restarting the program and performing phylogenetic analysis again. We would also recommend using the latest version of the MEGA software. The link for which has been provided in the description of this video. Hope this helps.

Thanks. You can use NCBI, Phytozone, or uniprot.

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​@@BiologyLectures hi i have a question if I want to construct tree for 13 protein coding genes of fish .how I select genes from ncbi ..means I have to past all thirteen genes in for blast analysis..and then select the top sequences.. actually i m new in this field plz guide me

@@just_another_dreamer123 You can choose the accession number of genes that you want to use in your Phylogenetic analysis from NCBI. You need to mention the accession numbers you used in your method section of phylogenetic analysis. Here's a general guide to help you get started: Identify the genes of interest: Determine which specific protein coding genes you want to include in your analysis. This could be based on their functional importance, relevance to your research question, or any other criteria. For example, you might choose genes involved in a particular biological process or genes that are commonly used for phylogenetic analysis in fish. Retrieve sequences from NCBI: Visit the NCBI website (www.ncbi.nlm.nih.gov/) and search for each gene of interest using the gene name or accession number. NCBI provides a vast database of genetic information, including DNA and protein sequences. Locate the relevant sequences for each gene and make note of their accession numbers. Sequence alignment: Perform multiple sequence alignment. Sequence alignment is necessary to identify the similarities and differences between sequences and to ensure accurate phylogenetic analysis. There are several tools available for sequence alignment, such as Clustal Omega, MAFFT, or MUSCLE. You can use any of these tools to align the sequences for each gene. And construct the tree as shown in the video.

@@BiologyLectures thank you so much for your reply .. actually i work on 13 protein coding genes...i construct phylogenetic tree for all genes one by one....by pasting my sequenced gene and retrieve other genes from ncbi for comparison But want to know if I want to construct tree for all the 13 protein of one sample not single gene..how can I ..so confused in this...

@@just_another_dreamer123 You can copy the sequences of all the prorein coding genes and paste it in the MEGA software as shown in the video. And construct the tree. Dont get confused. It is quite simple. All the best.