Body: <p>I have 25 individuals' whole-genome sequence (collected from 5 different locations) and after doing a variant calling analysis, I found 2734 SNP+INDELS marker (SNPs + INDELS = 2734 ). Then I plotted the PCA plot (pc1 and pc2) using variant calling data, i.e. raw SNPs.</p>
  <p>Now I am trying to interpret the population structure.</p>
  <p>Here I can see that these individuals from different locations are genetically different and there is no difference between individuals from the same geographic foci.</p>
  <p>Are there any other things that I can report?</p>
  <p>EDIT: Each circle(except green) represents a cluster of 4 individuals (that overlap with each other) and the green dot represent one individual</p>
  <p><a href="https://i.sstatic.net/PCHzx.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/PCHzx.png" alt="enter image description here" /></a></p>
  <p>Then I calculate nucleotide diversity (π) values (across the whole genome) of each cluster observed in PCA plot: What is best way to show that information?</p>
  <p>The mean pi value of each cluster:
  1 5.61 E-05
  2 4.76E-0.5
  3 0.00045
  4 2.56e-05
  5 4.69e-0.5</p>
  <ol>
  <li>Is there any test that should I perform to see if there are any significant differences, such as panmixia, migration or neutrality?</li>
  <li>Can someone explain to me how to interpret and report the finding from PCA and π?</li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-18T15:22:21.077Z
Comments.Text: What's being shown on the PCA plot? I'd have expected to see the 25 samples, but it looks like you're plotting just the cluster centers, which makes it impossible to evaluate how tightly grouped the samples are. What's the meaning of the inner green circles?
Comments.UserDisplayName: Nuclear Hoagie
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-18T15:25:46.583Z
Comments.Text: HI, the sample that I plotted overlap each other that's why it is looking like that. Each circle represent (except green) a cluster of 4 individuals (that overlap) and the green dot represent one individual
Comments.UserDisplayName: Ashar
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-18T15:53:23.207Z
Comments.Text: @NuclearHoagie I made changes to the original post.
Comments.UserDisplayName: Ashar
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-23T23:35:05.837Z
Comments.Text: when you say you are interested in population structure, what do you mean? why are you estimating pi within clusters? what is the meaning of the clusters? did you place the clusters together or are they the output of some procedure? Is there a reason that you are not using $F_{ST}$ between clusters, if they are pre-defined? Have you considered using STRUCTURE or another tool that does unsupervised clustering (not just PCA projection)?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-04-30T11:01:27.623Z
Comments.Text: I'm happy to answer this if @Ashar is still seeking a solution
Comments.UserDisplayName: M__
Tags: <phylogenetics><pca>
Title: PCA analysis and nucleotide diversity pi
ThreadText: # PCA analysis and nucleotide diversity pi
  
  (Asked by: username_0 on 2020-12-18)
  
  I have 25 individuals' whole-genome sequence (collected from 5 different locations) and after doing a variant calling analysis, I found 2734 SNP+INDELS marker (SNPs + INDELS = 2734 ). Then I plotted the PCA plot (pc1 and pc2) using variant calling data, i.e. raw SNPs.
  
  Now I am trying to interpret the population structure.
  
  Here I can see that these individuals from different locations are genetically different and there is no difference between individuals from the same geographic foci.
  
  Are there any other things that I can report?
  
  EDIT: Each circle(except green) represents a cluster of 4 individuals (that overlap with each other) and the green dot represent one individual
  
  [![enter image description here](https://i.sstatic.net/PCHzx.png)](https://i.sstatic.net/PCHzx.png)
  
  Then I calculate nucleotide diversity (π) values (across the whole genome) of each cluster observed in PCA plot: What is best way to show that information?
  
  The mean pi value of each cluster:
  1 5.61 E-05
  2 4.76E-0.5
  3 0.00045
  4 2.56e-05
  5 4.69e-0.5
  
  1. Is there any test that should I perform to see if there are any significant differences, such as panmixia, migration or neutrality?
  2. Can someone explain to me how to interpret and report the finding from PCA and π?
  
  **Tags:** phylogenetics, pca
  
  > **Comments:**
  > **username_1**: What's being shown on the PCA plot? I'd have expected to see the 25 samples, but it looks like you're plotting just the cluster centers, which makes it impossible to evaluate how tightly grouped the samples are. What's the meaning of the inner green circles?  
  > **username_0**: HI, the sample that I plotted overlap each other that's why it is looking like that. Each circle represent (except green) a cluster of 4 individuals (that overlap) and the green dot represent one individual  
  > **username_0**: @username_1 I made changes to the original post.  
  > **username_2**: when you say you are interested in population structure, what do you mean? why are you estimating pi within clusters? what is the meaning of the clusters? did you place the clusters together or are they the output of some procedure? Is there a reason that you are not using $F_{ST}$ between clusters, if they are pre-defined? Have you considered using STRUCTURE or another tool that does unsupervised clustering (not just PCA projection)?  
  > **username_3**: I'm happy to answer this if @username_0 is still seeking a solution  
  
  ---
  
  ## 0 answers
  
  