Sunday, June 21, 2015

The 5 most rewarding papers I have ever written

Last week I wrote about the five most difficult papers I have ever written or had a hard time publishing. So today I am writing about the five "easiest"/rewarding papers I have written. I should be quick to point out that I am not talking here about short notes or small synonymy papers but rather about papers that somehow seem to flow easy, or the writing process was a breeze, or the end result was very rewarding... just read below.

Papers are in chronological orders.

1. Chatzimanolis, S., M. S. Engel, and A. Trichas. 2002. Taxonomic changes for the Aegean species of the Mediterranean darkling beetle genus Dendarus (Coleoptera: Tenebrionidae). Journal of the Kansas Entomological Society 75(4): 259–267.

I still remember with glee the writing process for this paper. I had several new taxa of Dendarus to describe and several subspecies to raise to the species level before submitting the phylogeny paper and I was really not sure how to proceed [this was my first "new species" paper]. I was sitting in my office around 11am and Michael Engel stopped by to say hi. I told him that I was lost and he was like, "well, let's do this". We were writing for about 8 hours straight, we went for dinner, and then came back and finish the paper! To this day, this was one the best writing days ever. As a side note, Michael would often abandon his day plans to help students whenever needed.

2. Chatzimanolis, S. 2005. Phylogeny of the neotropical rove beetle genus Nordus (Coleoptera: Staphylinidae) with a special reference to the evolution of coloration and secondary sexual characters. Systematic Entomology 30: 267–280.

I was expecting this paper to have a hard time in review. Not sure why - and don't get me wrong, I think this is a pretty good paper. I just wasn't expecting to hear back from the editor within nine (9!) days after I submitted the paper telling me that both reviewed had positive things to say about it. I think nine days is still the fastest (positive) response time I had from a journal and that beats all the ones claiming fast response times (e.g. Zootaxa, Zonkeys, Biodiversity Data Journal and PeerJ). I don't remember much about writing  this paper but it was part of my PhD thesis, so it was written over a period of a couple of years.

3. Chatzimanolis, S., and J. S. Ashe. 2005. Revision and phylogeny of the neotropical genus Philothalpus (=Eugastus Sharp and Allostenopsis Bernhauer) (Coleoptera: Staphylinidae: Xanthopygina). Insect Systematics and Evolution 36: 63–119.

I really miss Steve and I really miss writing papers with him. Steve passed away in 2005 and for a couple of years I have been trying to write a blog post about him, but it is still very hard to do so. Steve was my major professor and (by his request) he did not take automatic authorship in my PhD papers. The few papers we coauthored together are the ones we really worked together. And boy, Steve and I had an awesome co-author relationship: we divided and conquer, splitting the manuscript tasks and we produced (amazing, if I may) papers fast and efficiently. In this paper we described 17 or so new species of Philothalpus  and the paper took just a few months to complete (I am not including here the prep work to figure out the new species).

4. Chatzimanolis, S. 2012. Zackfalinus, a new genus of Xanthopygina (Coleoptera: Staphylinidae: Staphylinini) with description of 20 new species. Annals of the Carnegie Museum 80(4): 261-308. 

This was not an easy paper to write (20 new species) but it was a very rewarding experience: publishing color photographs for every single species and really taking the time to illustrate/photograph every single important character. Also, I think this paper more than any other (and for reasons that I do not really understand) established me as an expert in Xanthopygina among my fellow rove beetle systematists. Now, the paper took a year plus from the time it was submitted to publication, but that's not really important here.

5. Chatzimanolis, S. 2014. Darwin's legacy to rove beetles (Coleoptera: Staphylinidae): a new genus and a new species including materials collected on the Beagle's voyage. Zookeys 379: 29-41.

I have written before here and here about how I ended up describing a taxon collected by Darwin. The paper was really straightforward to write (a simple new genus and new species description) with a bit of sauce (what other rove beetles had been collected by Darwin) but it got a lot of media attention (a summary of media mentions is given here). Still, that's not the reason why this paper is here. It's here because I ended up chatting via email with David Sedaris about it (the species epithet is in his honor) and that was enough to make my day/year/decade.

Friday, June 12, 2015

The 5 most difficult papers I have written so far

I recently passed the 50 published papers mark (sure, no such benchmark exist, it just feels nice) and looking back at the list I saw some papers that were horrible to write (or the peer review process was awful) and others that were really a piece of cake. Of course, for the majority of the papers the process was fun but… normal. Anyway, I decided to write a couple of posts, first this one about the 5 most difficult papers I have written and another one later about the 5 easier ones.

First of all, some data: the complete list of my papers can be found here (pdfs included). In the old days of graduate school/postdoc, I used to write my papers using Word. Nowadays, I am using Scrivener and Pages (or Google Docs if I have coauthors). Before I got tenure I was trying to publish my papers in the “best” possible journals. After tenure, I have focused my attention more to open access journals or journals that do not have byzantine instructions to authors (with some exceptions, I am looking at you Koleopterologische Rundschau).

So here is the list of the 5 most difficult papers (in chronological order) to write/take through peer review. As a side note, this list include only papers that I wrote as the first author. Some other papers where I was the second/middle/last author had troubled histories but I do not think it is my place to discuss those.

Nordus fungicola
I think I lost count how many times this paper was rejected before it found its home in the Annals. The whole process was very discouraging to a young graduate student and there were moments I thought this paper will never get published. But the core of my PhD committee (“the readers” the late Steve Ashe, Michael Engel and Mich (Charles Michener) were very supportive and really helped along. I think some edits by Michael after a few rejections really helped that paper.  I believe I was trying to get this out during the second or third year of graduate school, so I really did not know how to write a paper. Also, this was a descriptive natural history paper, and behavioral ecologists that were reviewing this paper really did not like it.

[I guess 2003 was a bad year?]  

This paper also went through a few rejections before it got published. The problem with this paper was that it started as my undergraduate thesis at the University of Crete. Steve Ashe was really pushing me to send it out even though it was not what I was doing in Kansas (also the paper is on darkling beetles while my PhD was on rove beetles). I started working on this paper the second year I was in Kansas, and by that time I realized that my undergraduate phylogenetic analyses were crap. So I had to borrow many specimens from my undergraduate home (the Natural History Museum of Crete), recode many characters and redo the analyses. The whole process took more time than I want to admit. I first submitted it for review to the Zoological Journal of the Linnean Society, where the then editor (long retired now) sent it to just one reviewer who provided a three sentences review… The first sentence was that the phylogenetic part was crap, the second that the biogeographic part was crap and the third that the journal should not publish undergraduate work. How is that for constructive criticism to a graduate student? The next time I sent the paper for review I got smarter and removed any indication that this paper had started as an undergraduate thesis. 

The main paper that came out of my PhD, so I guess it really deserves to be up here. It just took forever to put that paper together and it was the first time I was putting together a major monograph as the first author. I went through the 99% rule (when you think you have done 99% of the work, but in reality you still have 99% to do) multiple times. The reviews were fine but the editor made me write a SECOND key for 38 species because he did not like my using of coloration and male-specific characters (whatever, I still hold a grudge, Klaus). That’s the closest I have been to losing it during a manuscript revision process. But to be fair, besides Steve Ashe, I do not think that anybody has ever read this paper as carefully as that editor. 

Lot's of resolution, right?

My first paper as a postdoc. It took a long time to become familiar with the phylogeography field before I could write this paper. Also, this is a paper where we reported more or less negative results (no phylogeographic structure - certainly not what we wanted to see). More troublesome was the fact that I had not done any science writing for more than a year. You would not know that by looking at my publication list, but as a (then) Greek citizen I had to do compulsory military service after I finished my PhD and before I started my postdoc (from Sept. 2004 to Sept. 2005). I had worked very hard as a graduate student to make sure that there would be no years without any publications, but when I started in Santa Barbara my writing skills were rusty to say the least. Mike Caterino had to teach me almost from scratch how to produce a sound scientific paragraph. 

I started writing this paper in 2009. I could not make one my coauthors respond to me requests/comments for almost a year due to some issues. This paper was in prep stage for almost three years. On top of that, when the paper came out (it got glowing peer reviews) I realized that some people really did not (and still do not) like the paper. Long story short, some folks think that what we described as a rove beetle is not rove beetle. I will not go into the details here (perhaps another blog post) and I still stand by this paper, but those issues almost caused permanent damage to some long collaboration/interactions with colleagues.