Question: How to interpret a phylogenetic tree
gravatar for wuqingkuangsha
11 months ago by
wuqingkuangsha20 wrote:

How to interpret a phylogenetic tree? How to answer questions like what is the evolutionary history of an organism? I did some search but most of the articles basically just say the evolutionary history represented by the tree. It's true but my question is about how to describe a phylogenetic tree in a language that looks professional and academic. You can't just tell me the information is embedded in the tree and just look at it.

phylogeny • 486 views
ADD COMMENTlink modified 11 months ago by Mensur Dlakic6.5k • written 11 months ago by wuqingkuangsha20

Interpreting a tree is less about reading the tree, and more about defining the question you’re asking of it.

Once you have a good question or hypothesis, it should be reasonably simple (in most cases) to say what it tells you about what you thought.

ADD REPLYlink written 11 months ago by Joe18k

I noticed that parts of my post were deleted without an explanation. Several complete posts that were part of this thread were also deleted without any explanation.

Is it part of standard procedures and approved actions for Biostars administrators to censor text and delete whole posts without explaining?

ADD REPLYlink written 11 months ago by Mensur Dlakic6.5k

Yes. We routinely tidy up discussions which aren't relevant to the OP.

ADD REPLYlink written 11 months ago by Joe18k

I have seen daily examples of administrators tidying up discussions and understand why it needs to be done. I appreciate that work very much, and it was my impression that non-trivial edits are communicated to users to help with future posts. My question was specifically about deleting whole posts without an explanation.

Given the effort needed to write a post, I would hope the administrators consider it worthwhile to explain why it was deleted. Of course, this is assuming that the post was not offensive or inappropriate in a way that is blatantly obvious. Explaining why the post was deleted promotes the culture of learning, as it provides feedback to the poster regarding the content that is not acceptable. This, in turn, saves time for all of us.

Also, misunderstandings are less likely when an explanation is given. I like to think that administrators are not deleting my post because I was criticizing their interactions with posters, but I still would not mind getting my assumption confirmed.

ADD REPLYlink written 11 months ago by Mensur Dlakic6.5k

Meta-discussions often confuse and detract from the original topic, which is why we discuss these things on slack. To new users, we do leave some comments on proper etiquette/formatting tips, but experienced users such as yourself are invited to be part of our slack community where we discuss these meta topics. I can see that your account became inactive a few weeks ago. Would you reconsider joining us there to discuss these issues?

ADD REPLYlink written 11 months ago by RamRS30k

Generally speaking, where edits are made, we will usually leave a ‘signature note’ from the mods/admins, if they could potentially change the meanings etc (but not for code formatting etc).

We don’t always (though usually do, and probably should have in this case) explain why we delete one or more comments/answers. Generally though, it is cleaner simply to delete everything, and us leaving another comment explaining the content that we removed, when that content can no longer be seen, can sometime just confuse matters and contributes to the messy-ness of the thread.

We are all grown ups :) we didn’t delete the content because we are Gestapo-like and can’t take criticism, and its no reflection on the content or meaning of your (and our) posts that were deleted - it is purely to serve the OP in keeping the thread clean such that they, and users that find the thread in future, don’t have to wade through a lot of off topic meta-chat.

As Ram points out, this one of the reasons we maintain a Biostars Slack group now, so that the meta-chat can be dealt with in real time, whilst leaving BioStars posts to focus on the meat of the OPs original query.

We don’t get it right 100% of the time and are only human after all, but we do aim to try and be consistent, as well as ‘minimally censorious’.

ADD REPLYlink written 11 months ago by Joe18k

I appreciate your thoughtful responses, especially so because I understand that you want to keep these kinds of discussions from invading on original posts. I'd like to do the same, but I don't know any other mechanism on Biostars for these topics. I appreciate the offer to re-join the Slack channel, but I don't think that format works for me.

I don't mean to beat a dead horse, but there are all kinds of inconsistencies in how administrative issues are handled. Without revisiting issues I brought up in other threads, I'll briefly make a point about deleting meta-discussions. Here is an example of a thread that included name-calling, subtle and not so subtle personal attacks, all kinds of detours from the original post, and yet not a single word in that thread was deleted or edited to the best of my knowledge. I should also add that multiple administrators participated in that thread, so it isn't like it flew under the radar. When a discussion like that stands unaltered - as I think it should, for posterity - it feels like an over-reach to alter my post that was on-point and to delete bunch of other posts without explaining. Those deleted posts, by my estimation, had an acceptable exchange of opinions that was not out of line compared to other posts of Biostars. At the very least I think there is a discrepancy in individual admin criteria of what posts should be deleted. If there is no universal agreement what posts should be deleted, could there be a universal agreement that all deletions should be explained? If the goal is to keep the thread clean, a personal message would have done the trick in my case.

Beyond the matter of consistency, deleting posts is dismissive by its nature, and doing so in fait acompli fashion only heightens the feeling. By the way, it is not the first time that I felt one of the admins was dismissive towards me - c'est la vie.

One last thing before I close, as I may never write another post about these topics. It is great to be collegial and support the fellow admins, as evidenced by this thread. Even though a third person apparently tidied up this thread, two fellow admins stepped up to explain the rationale behind their action. That's nice, but I urge all admins to please consider, as a general matter, that some actions of other admins are not right simply by virtue of their title or positional affiliation. There is a fine line between collegiality and blind loyalty, and it is not out of the realm of possibility that on occasion posters may have a better case than admins.

ADD REPLYlink written 11 months ago by Mensur Dlakic6.5k

We are aware there are inconsistencies. The admins and mods are drawn, voluntarily, from the contributors on the site. We are, of course, not infallible, and we welcome people to keep us in check in constructive ways (though we do prefer these discussions to be had on Slack as we mentioned, since unlike StackOverflow, we have no ‘BioStars Meta’ forum for these discussions, and they’re better resolved in real time usually).

The particular thread you link to was an especially egregious example. I will say this, that in my opinion, the comments in that thread are actually pertinent to the original point. We surmised, based on the reaction to many comments, that the poster didn’t have, at least in my estimation, a genuine interest in getting honest and constructive feedback from the community. Given the tortuous route that conversation took, it would not have been a trivial one to clean up (limitations in the biostars engine for instance, would mean some comments end up out of order etc), unlike this thread. I would also point out that the ad hominem elements of that thread stemmed from the OP themselves, and we tried several times to keep the thread civil and on topic as the record shows.

Part of the reason we recommend slack, is that moderator actions are discussed beforehand. In the case of this thread, we had a poll to decide whether or not to clean this thread up which was (I believe) unanimous.

To reiterate, its not that the exchange in those posts wasn’t ‘appropriate’ for the forum, its just that it was only a small exchange, easily cleaned up, everyone can move on, and the thread then remains as a neat repository of knowledge for future users. The discussion did not add much to the thread, and the purpose of these threads is not to keep a verbatim record of the thread as it unfolds necessarily - its not uncommon for moderators to tidy up old threads to preserve just the relevant information for instance. Biostars has no facility for personal messaging (another reason we use slack) unfortunately.

Just finally, this isn’t about admins backing one another up (we regularly disagree about how to proceed with threads, and in fact, this thread is still under discussion) and if necessary, reverse the decisions if overruled. Most, if not all, of the mod actions we make are consensus ruled. That said, our moderator community is selected from all over the world, and thus there is some merit to personal opinions and perspectives, particularly when it comes to subtleties in culture or language.

Personally, I’m from the UK, and am no snowflake. We’re no strangers to sarcasm or quick wit, however, I stand by my original stance that the comment could have been interpreted worse by those that might not have understood the jest, which can contribute to the forum seeming hostile, like StackOverflow, which is very much not what we want. The way in which you approached the quote is unfair if the OP does not understand that its a joke, especially if the language barrier is sufficient that they thought they were expressing themselves correctly.

ADD REPLYlink written 11 months ago by Joe18k
gravatar for Mensur Dlakic
11 months ago by
Mensur Dlakic6.5k
Mensur Dlakic6.5k wrote:

You can't just tell me the information is embedded in the tree and just look at it.

Phylogenetic trees represent evolutionary distances between tree members as deduced from residue substitution patterns. In case it is not obvious, a distance between any two tree members is the shortest path obtained by tracing from one branch to another. From trees we can surmise not only how related tree members are on a relative scale, but also the order of events that shaped their evolutionary history. This is rarely perfect because events other than mutations and indels contribute to evolution, for example horizontal gene transfer.

It is worth mentioning that a phylogenetic tree represents a hypothesis (a reconstruction, if you will) based on available data. There are statistical measures, both at the level of individual branches and globally, of how likely this hypothesis is to be accurate. Adding or subtracting members can and does lead to different trees.

ADD COMMENTlink modified 11 months ago by Devon Ryan96k • written 11 months ago by Mensur Dlakic6.5k

Just a quick clarification for wuqingkuangsha or others: trees can be built based on nucleotides and even phenotypic traits, not strictly residues.

Edit: I had a lot more about ML and Bayesian approaches and why this matters, but I just deleted it because it's a bit beyond the scope of the question. OP, free to ask in a new question if interested in how trees are estimated generally.

ADD REPLYlink modified 11 months ago • written 11 months ago by Brice Sarver3.5k
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