Evolutionary Biology Online Journal Club

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Season 2, Meeting 2 – Consistency & Consensus in Taxonomy

After last session’s discussion on species concepts/definitions, people thought it might be worthwhile talking about species from a taxonomist’s point of view. There aren’t many papers I know of that talk about the taxonomic process, but if people have questions I’ll be happy to answer what I can from my experiences.

However, I did find a paper that I think does a good job of discussing some of the issues that were brought up last time, and introduces a few more ideas on what a species is from a taxonomists viewpoint, and how that viewpoint differs between individuals:

Vane-Wright, R.I. 2003. Indifferent Philosophy versus Almighty Authority: on consistency, consensus and unitary taxonomy. Systematics and Biodiversity 1 (1): 3-11. doi:10.1017/S1477200003001063 (PDF here)

Vane-Wright refers back to a short commentary that was published in Nature a few months prior that might also be of interest:

Godfray, H.C.J. 2002. Challenges for taxonomy. Nature, 417: 17–19. doi:10.1038/417017a (PDF here)

Anyways, Vane-Wright discusses the nomenclatural plight of a group of African butterflies and how definitions of the species of interest have changed through time and with differing research opinions/objectives. Everything from creationism to cladism is discussed, and the author proposes a new hierarchical system that only serves to complicate matters in my mind. I think it should be a pretty interesting discussion, and I’m looking forward to hearing what everyone else thinks of it.

P.S. There was some discussion about how taxonomy can affect conservation last time as well, so I thought I’d point people to this paper which does a nice job of discussing the issue:

Mace, G.M. 2004. The role of taxonomy in species conservation. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 711-719. doi:10.1098/rstb.2003.1454 (PDF here)


Planning our second meeting

Screen Shot 2013-02-07 at 10.36.01 AM

It seems from the poll that most of you would like to go back to Google+ Hangouts after our first meeting, so we’ll do that for next time. Make sure you add our google+ page to your circles, otherwise you won’t get the invitation for the videochat!

Remember that even if you didn’t join the first meeting, you’re more than welcome to join the following ones! Just introduce yourself in the forum page!

Now we need to decide on a topic and a volunteer to lead the discussion. I made a list of topics that were brought up:

  • Speciation and Taxonomy 
  • Sympatry, allopatry and the geography of speciation
  • Ecological speciation and adaptive radiations
  • The genomics of speciation (the Ficedula flycatcher paper might be a good starting point)
  • Population genetics, demography, and speciation
  • Sexual selection, behavior, speciation and non-adaptive radiations (sneaked this one in!)
  • Cospeciation and coevolution

We can add more topics as they are suggested, but if we’re meeting every other meeting those topics could well fill our schedule. Let me know if they sound good or if there are some of these you’re not really that interested in as well!

I got a couple links that might provide us inspiration for topics and/or ideas for papers:

So now we need volunteers and paper suggestions! I agree with Sam that we should rather have a Taxonomy-centered discussion sooner than later, so if nobody volunteers until tomorrow I’ll just go ahead and “volunteer” Morgan Jackson to choose a paper and lead the discussion 🙂

We should have a paper chosen by Monday the latest, giving us a week before next meeting on Monday February 18th, 4:30PM EST!


Species Concepts for Conservation – Nature 494

As if on cue, Nature published a short Correspondence letter this week which talks about the effect that species splitting is having on mammal conservation. You can read it online here (paywall, so also here).

Personally, I don’t really like it when someone says we should be stemming our research to fit political ideals, and feel that the authors are just trying to get other taxonomists to conform to their own ideas of what a species is. It is interesting to see how the Biological Species Concept is pitted against Phylogenetic Species Concepts however, and it’s clear that some people are not as open to hybrid definitions/concepts like we discussed earlier this week.

What do you think? Should we restrict changing species concepts of threatened species, or are there other ways to approach this problem without throwing taxonomy under the bus?
Zachos F.E. (2013). Taxonomy: Species splitting puts conservation at risk, Nature, 494 (7435) 35-35. DOI:

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Archive of Papers Discussed

Below is an archive of the papers we have discussed to date, with links to our recorded video discussions. We will try to keep this archive updated, but if (read: when) we fall behind, you can always find a link to each paper somewhere in the main thread of the blog, and all the video discussions are archived here.

Disclaimer: if you are citing any of these papers, I advise against copying-and-pasting the references below. The references are not in any particular format, and though we do our best, we cannot ensure that they are 100% accurate and free of typos.

Season 2: Speciation (February-May 2013)

2.3: Geography of Speciation (video discussion)

a) Fitzpatrick, B. M., Fordyce, J. A. and Gavrilets, S. (2008). What, if anything, is
sympatric speciation?. Journal of Evolutionary Biology, 21: 1452–1459.
b) Mallet,  J., Meyer, A., Nosil, P.  Feder, J. L. (2009). Space, sympatry and
speciation. Journal of Evolutionary Biology, 22: 2332–2341.

2.2: Consistency and Consensus in Taxonomy (video discussion)

a) Vane-Wright, R.I. (2003). Indifferent Philosophy versus Almighty Authority:
on consistency, consensus and unitary taxonomy. Systematics and Biodiversity
1(1): 3-11. doi:10.1017/S1477200003001063 (PDF here)
b) Godfray, H.C.J. (2002). Challenges for taxonomy. Nature, 417: 17–19.
doi:10.1038/417017a (PDF here)

2.1: Overview of Species Concepts (and how they relate to each other)

de Queiroz, K. (1998). “The general lineage concept of species, species criteria,
and the process of speciation.”  in  Howard, Daniel J., and Stewart
H. Berlocher, eds. Endless forms: species and speciation.
Oxford University Press, USA, 1998.
(no video of discussion available–sorry)

Season 1: Assorted Topics (September-November 2012)

Brian K. Hall, Ryan Kerney. (2011). Levels of Biological Organization and
the Origin of NoveltyJournal of Experimental Zoology B: Molecular and
Developmental Evolution
 318(6): 428-437.
(video discussion)

Douglas J. Emlen, Ian A. Warren, Annika Johns, Ian Dworkin, Laura Corley Lavine.
(2012). A Mechanism of Extreme Growth and Reliable Signaling in Sexually
Selected Ornaments and WeaponsScience 337(6096): 860-864.
(video discussion)

Forister, M.L., Gompert, Z., Nice, C.C., Forister, G.W. and Fordyce, J.A. (2011).
Ant association facilitates the evolution of diet breadth in a lycaenid butterfly.
Proc Roy Soc B 278: 1539-1547.
(R code graciously provided by the author can be found here)
(video discussion)

Peter Nonacs. (2011). Kinship, greenbeards, and runaway social selection in the
evolution of social insect cooperationPNAS 108, Supplement 2.
(video discussion)

Andrew F. Hugall,  Devi Stuart-Fox. (2012). Accelerated speciation in colour-
 birdsNature 485: 631-634.
(video discussion)


Planning next meetings – your thoughts

Thanks everyone who showed up for the fist meeting of the year! Was great to hear what you all had to say. I thought the experiment with Shindig was quite interesting, had its pros and cons but especially after we got the hang of it things went a lot more smoothly (as would be expected when trying out a new platform). But I’d like to hear from you guys before we decide what to do. I’m leaving a poll at the end of this post, but please also use the comments section in this post to share your thoughts!

Personally I think it’s a promising platform, but the bandwidth issue seems to be a bit limiting. I thought the “only 2 at once” was going to be a big problem, and it may have made the discussion a bit centered in the people that were up there, but still a lot of people did come up and speak, which is pretty awesome. Google Hangouts may be a bit more dynamic, but there’s the “10 people limit” (which we can partially get around using text chat, which is not the same I guess….).

Another problem is that I tried to record a screencast of the discussion to post, but I failed. Even though I set the program the right way (and tested earlier), it only recorded my audio, and nothing that everybody else said. As I assume you’ve all have heard enough of my voice, I won’t post it online. Google Hangouts does streamline this, recording and posting to youtube automatically.

What do you think?

For the next meeting. We need a volunteer to choose a paper! What would you guys want to talk about? I thought about a couple topics – The genetics of speciation, Ecology of speciation, linking population dynamics to diversification, micro + macroevolution, hybridization – but I’d really like to hear from you. So please someone volunteer in the comments to choose a paper 🙂 and share what topics you’d be interested in discussing!

Thanks again! Looking forward to the next meeting!

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Some information for today’s meeting

Hopefully everyone is ready and as excited as I am for today’s first meeting of the Evolutionary Biology Online Journal Club! I think this will be a great group and a great topic for discussion. As you all know by now, we will be giving the Shindig platform a try this term. This will get us free of the 10 people limit and hopefully be a more open experience to everyone.

However, as would be expected of a change in platform, there are a couple of things that will be different, and that we need to take into consideration for it to work well. The main difference is that the Shindig videoconference does not offer an “open mic” debate, like in the Google hangout, where anyone could start talking at any moment and everyone will hear. Instead, there are up to two “active” debaters at any given point in time. I know this might sound kind of weird for a journal club debate, but on the other hand having some sort of structure might actually help if we do end up having more than 5 or 6 people, so we don’t run the risk of talking over each other. It may help us use our time better. But most importantly, anyone can join the active microphones at any time by pressing the “raise hand” button. The technical moderator from Shindig will then open the mic for you (or add you to a queue if there’s more than one).  In order for the journal club to work, it is really important that we try not to “shy out” and take part in the discussion! So don’t be afraid to “raise hand” and join in and share your thoughts and ideas! 🙂

Also, I believe Shindig offers a text chat as well, so we won’t have to use the IRC channel. Just click on the “IM” button that shows up when you hover your mouse over your picture, then select the “Shindig” tab in the window that shows up. This might be a good way of making a quick comment/question when someone else is talking.

In order to get acquainted with the platform, I recommend taking a few minutes and watching the videos below, that showcase how it works:

And, again, remember that this is an experiment with this new platform. After we’re finished with the meeting today, I will put up a poll and we can decide if it worked or not, and go from there. I do think it will be a cool experience, we just need to get used to the changes that come with the possibilities offered by the Shindig platform!

See you all at 4:30PM EST today!! (and don’t forget to RSVP following that link if you haven’t yet!)