Answers.Body: <p>The top phylogeny is likely mid-point rooted, but I suspect the rooting is fine. The lower diagram has been rooted on the query sequence. It is taxonomic analysis using 16S which in bacteria is considered to represent species delineation at a given percentage of divergence. I thought it was 5%, which is impossible based on the phylogram in the top picture.</p>
  
  <p>Bootstrap values lower than 80% mean that the clade is not supported (monophyletic group is a better term). The delineation between 10001 and 10013 against the massive ingroup of 13 16S sequences is robustly supported by bootstraps of 95% and 99%. The divergence between them is around 2%. There is no taxonomic distinction between the 13 16S sequences based on the phylogram.</p>
  
  <p>One question is whether this is full length 16S? If it is there appears to be a species designation confusion in the lower clade supporting 10001 and 10013 because it is identical to to Dermococcus species and there is no way to assess which one is valid, nor whether they are really members of the same species. The very small divergence suggesting in D. abyssis might also call this into question. 10013 is in fact a robust outgroup to 10001 and the three Dermococcus spp. but the genetic distance involved is small.</p>
  
  <p>However, this is not the major result. You have recovered what appears to be a large population (if that is how you sampled it) with close genetic homology to Dermococcus strain DSM20448. Given the complexity of species lineation within this genus it is impossible to say whether this represents the same species as DSM20448 but you could call it a "species complex". </p>
  
  <p>Overall the population structure (if that is how it was sampled) is heavily skewed towards a bacterial species which is hitherto received minimal attention. This population skew (if that is how it was sampled), could be reversed in different ecotopes/niches/ecoregions/patients? </p>
  
  <p>In summary, I wouldn't get caught up in systematics because in this genus its a bit messy. I would focus on the population structure and these results are very clear.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-20T21:09:21.153Z
Answers.Text: Thank you so much! It is only a partial sequence so the bootstrap being low isn't a surprise.
Answers.UserDisplayName: Erin Clingerman
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-20T15:22:08.817Z
Answers.LastActivityDate: 2019-02-20T15:22:08.817Z
Answers.UserDisplayName: M__
Body: <p>I constructed a phylogenetic tree using mole blast, and it created a neighbor joining tree, so I used the alignment of those sequences with mine (1-43) in mega with TN93+G+I model but I don't understand how to interpret why my species in question (29) is so much different (or maybe novel?).</p>
  
  <p>Attached is my original tree (Picture 1) and my bootstrap analysis (Picture 2):</p>
  
  <p><a href="https://i.sstatic.net/dG4SC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/dG4SC.png" alt="enter image description here"></a>
  <a href="https://i.sstatic.net/1syFE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/1syFE.png" alt="enter image description here"></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-19T19:58:53.030Z
Comments.Text: Are these the same tree with different roots? The first tree is probably rooted by middle point. How did you root the second tree?
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-02-19T20:20:05.377Z
Comments.Text: Yes that is correct. The interpretation is easy and relates to the population structure of two definite bacterial species within the same genus. I will provide a detailed interpretation shortly.
Comments.UserDisplayName: M__
Tags: <phylogenetics><phylogeny>
Title: Help interpreting my phylogenetic tree construction of bacterial species in same genus
ThreadText: # Help interpreting my phylogenetic tree construction of bacterial species in same genus
  
  (Asked by: username_0 on 2019-02-19)
  
  I constructed a phylogenetic tree using mole blast, and it created a neighbor joining tree, so I used the alignment of those sequences with mine (1-43) in mega with TN93+G+I model but I don't understand how to interpret why my species in question (29) is so much different (or maybe novel?).
  
  Attached is my original tree (Picture 1) and my bootstrap analysis (Picture 2):
  
  [![enter image description here](https://i.sstatic.net/dG4SC.png)](https://i.sstatic.net/dG4SC.png)
  [![enter image description here](https://i.sstatic.net/1syFE.png)](https://i.sstatic.net/1syFE.png)
  
  **Tags:** phylogenetics, phylogeny
  
  > **Comments:**
  > **username_1**: Are these the same tree with different roots? The first tree is probably rooted by middle point. How did you root the second tree?  
  > **username_2**: Yes that is correct. The interpretation is easy and relates to the population structure of two definite bacterial species within the same genus. I will provide a detailed interpretation shortly.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2019-02-20. Score: 3
  
  The top phylogeny is likely mid-point rooted, but I suspect the rooting is fine. The lower diagram has been rooted on the query sequence. It is taxonomic analysis using 16S which in bacteria is considered to represent species delineation at a given percentage of divergence. I thought it was 5%, which is impossible based on the phylogram in the top picture.
  
  Bootstrap values lower than 80% mean that the clade is not supported (monophyletic group is a better term). The delineation between 10001 and 10013 against the massive ingroup of 13 16S sequences is robustly supported by bootstraps of 95% and 99%. The divergence between them is around 2%. There is no taxonomic distinction between the 13 16S sequences based on the phylogram.
  
  One question is whether this is full length 16S? If it is there appears to be a species designation confusion in the lower clade supporting 10001 and 10013 because it is identical to to Dermococcus species and there is no way to assess which one is valid, nor whether they are really members of the same species. The very small divergence suggesting in D. abyssis might also call this into question. 10013 is in fact a robust outgroup to 10001 and the three Dermococcus spp. but the genetic distance involved is small.
  
  However, this is not the major result. You have recovered what appears to be a large population (if that is how you sampled it) with close genetic homology to Dermococcus strain DSM20448. Given the complexity of species lineation within this genus it is impossible to say whether this represents the same species as DSM20448 but you could call it a "species complex".
  
  Overall the population structure (if that is how it was sampled) is heavily skewed towards a bacterial species which is hitherto received minimal attention. This population skew (if that is how it was sampled), could be reversed in different ecotopes/niches/ecoregions/patients?
  
  In summary, I wouldn't get caught up in systematics because in this genus its a bit messy. I would focus on the population structure and these results are very clear.
  
  > **Comments:**
  > **username_0**: Thank you so much! It is only a partial sequence so the bootstrap being low isn't a surprise.  
  
  ---
  
  