It Figures

One of the weirder dynamics of trying to finish a PhD dissertation in Hades is the cycle of sending out a draft, waiting for comments, sometimes for several months, then getting the chapter back after one has already moved on to many other things. I chose to do a PhD in four different quantitative and statistical method domains, which means that, for example, getting the chapter on population viability of my study species back after a couple months means cranking up all the rusty machinery related to that analysis. Fortunately, the R code in which I have done the entire PhD is saved in three different places and is fairly easy to run after refreshing my memory. 

Yesterday was involved with learning how to make a particular, very complex figure for an entirely different chapter, the one on the historical biogeoraphy of the genera I studied. This kind of study uses a phylogeny (in my case, a molecular one) to make hindcasting predictions of where the most likely ancestral ranges of current taxa were. It helps a lot of one has a few geospatially located fossils, but the Cactaceae does not cooperate in that regard, I did have some well-supported time calibrations from a paper by Arakaki et al. (2011), and calibrated a Bayesian analysis in a program called BEAST (Bayesian Evolutionary Analysis Sampling Trees; a companion program that prepares the input files is called BEAUTi. Get it? So droll). Anyway, this is some incredibly complex shit. It takes like a whole day to even format the input file with the proper parameters for one's data. Even so, there are a great many options to customize the analysis, and then the recommended number of iterations of the algorithm is 20 million, so each analysis takes two to three days on a laptop. I ran 16 analyses in all, just changing this or that each time, such as the nucleotide substitution rate, or the prior distribution of the rate of substitution on ancestral nodes, etc. Yikes. 

Anyway, as has been typical with a lot of this PhD, the two committee members who reviewed the biogeography chapter both agreed that the ancestral range reconstruction needed more than just a color coded phylogenetic tree, but also a color coded map. As of about 7:00 a.m. yesterday I had no idea how to create a map with the ecoregions I had used for ancestral ranges, and then fill each of those ecoregions with a color identical to the color represented on the nodes of the tree I had. I emailed a Mexican botanist friend of mine who had done a nice figure in a paper that just came out, and he gave me a few tips. He had created his in Corel Draw, but I downloaded a trial version of that and it seemed horrifying, so I found a way to do it in ArcGIS, the high-octane, user-baffling proprietary GIS software from ESRI. Also horrifying, but I am familiar with it. I have a free student license for this, which is great, because a home license is $1200. 

I must have excellent intuition on ecoregions, because, without knowing it, the nine regions I chose as ancestral ranges for my group of cacti are actual ecoregions, specified by the World Wildlife Fund and others. Well, three of the ecoregions required making a composite of several smaller regions, but they all fit together into the actual regions I had used. That's lucky, because it meant that they are available as map layers (crazy-ass files called "shapefiles") that can be added to a map project in ArcGIS. The color values can be read directly from the tree I generated in a program called RASP (Reconstructing Ancestral States from Phylogeny) and then, in ArcGIS, the fill color can be set to be identical. But this whole process took me several hours, since I didn't know how to do any of it. Here's the resulting map, with its garishly contrasting colors, which, alas, for scientific figures, is recommended. 

It seems like it would be a simple task, to create a color coded map like this. Well, come to think of it, now that I have done it, it would be the second time. Until I forget how to do it. In other words, by the time I get the next round of comments. I am still trying to figure out how to make a clear, high resolution legend for the map, and trying to fit this map and the phylogenetic tree (which has 88 taxa) on a single 8.5 X 11 page with 1 inch margins is a weird proposition. Actually, I know how to make a great legend for the map, but it involves redoing the entire map with the shapefiles renamed according to my ecoregions, and I lack the gumption today. 

Things are moving, however slowly. The species distribution modeling and climate change chapter is on its way to PeerJ, I think; still waiting on my committee member co-author for the green light to prep that one for submission. The molecular phylogeny paper is supposedly going to be submitted to Taxon, the super heavyweight systematics journal, published by the International Society of Plant Taxonomy. After the molecular phylogeny paper is accepted, the biogeography paper will probably be submitted to New Phytologist or the Journal of Biogeography, not sure. I am simultaneously preparing manuscripts for journal submission while finishing the PhD dissertation revisions. Unfortunately, dissertation chapters have to be significantly edited to be submitted to particular journals, a non-trivial amount of work. 

A lot of the rest of my life remains on hold. Waiting to hear back from two post doc apps. Putting together teaching apps. Intending to pre-qualify for a car loan but never actually filling out the applications. Intending to meditate and not meditating. Intending to work out and not working out (much). Part of the Hanged Man quality of life right now is the unrelenting heat, still in the triple digits. I am eager for it to cool off. I'm entirely ready to leave here, to leave Hades. But pushing does nothing at all. It is moving at the rate that it is moving. I can only show up and do my best.