Category Archives: Summaries

GeoRange: an R package for calculating geographic range

One thing that I wasn’t expecting going into grad school was the amount of coding I would do. I took an Intro to Programming in Java during my 2nd year in undergraduate, which I enjoyed, but otherwise never thought much about it. That changed during my master’s work when I had to write some of my own code in the R Programming Language for some specialized tests. I’ve since taken a course on data analysis in R and another focusing on Python and written A LOT of R code for research. Even though I don’t consider myself any kind of coding expert in R I’ve gotten to the point where I think other people might actually find some of the functions I’ve written to be useful. So, I’ve written and submitted to CRAN a package dubbed GeoRange which should be available for download shortly if it isn’t already.

 

Quick thank you to Dave Bapst for his advice and encouragement in publishing R packages. The whole process was made much easier by this online tutorial.

 

GeoRange is for calculating and analyzing six different methods of geographic range from point occurrence data (i.e. latitude and longitude). It was born from my interest in geographic range as it relates to extinction risk. Very quickly, all else being equal a species that is more widespread across the Earth is less likely to be wiped out by stochastic events than one with a small range (Jablonski 2005). For example, a species confined to a single island in the Caribbean might be killed by a single hurricane season whereas it’s nearly impossible to wipe out all individuals of a species that occurs across the Atlantic. Pretty much all the geographic range measures in the package can be done (in some cases more efficiently) within ArcGIS but I didn’t do use it because I am not really a fan of ArcGIS to put it mildly. I can use it but the system always seems very glitchy and opaque for my tastes and data analysis can be a hassle. I was going to end up doing some analyses in R anyway so I figured I might as well do everything in R.

 

The actual measures of geographic range include the convex hull area, maximum pairwise distance, latitudinal range, longitudinal range, X x X degree cell count, and minimum spanning tree distance. The first five are fairly standard measures that are commonly used in extinction analyses but the minimum spanning tree (MST) may be unfamiliar to people, even those that study extinction. Essentially, the MST finds the most cost-effective way to connect all points without ever creating a loop, a problem similar to the Traveling Salesman Problem. Originally the MST was used to find the most efficient ways to lay down power-lines with the cost between points corresponding to the cost of building. In terms of geographic range the cost is the great circle distance between points and thus the MST represents the minimum distance a species must have traveled to have reached all points. That might include crossing impassable terrain and is unlikely to represent the actual path or distance traveled but it still seems to be an excellent correlate of extinction risk, especially after accounting for sampling (Boyle et al. 2017). Not sure why this is yet except that it better captures other factors, like abundance and fragmentation, that are associated with extinction risk.

MST&CH_100pts_UShape

Figure 1. Horseshoe-shaped distribution (thick black outline) with 100 random points generated. Showing the minimum spanning tree (thin black lines) and convex hull (blue outline) showing the stark difference in methods for certain shapes.

            For analyses of multiple taxa GeoRange is set up to work with capture matrices and can work directly with data from the Paleobiology Database via the downloadPBD function in the velociraptr package.

There are some known limitations with this package that I’m looking to fix in some future updates. A major issue is that calculating the MST takes a long time for more than 1000 points. The PlotMST function doesn’t account for points connecting around the prime meridian so that creates off lines that jump across the plot. The CellCount function isn’t equal area cells, so high latitude cells are stretched compared to equitorial ones and similarly the random point generation functions RandRec and RandHorseShoe don’t account for the stretching of lat/long area with latitude. There are lots of little tweaks to increase user options and expand functionality but for now I’m happy to get some feedback on the work and keep up my coding skills.

References

Boyle, J. 2017. GeoRange: Calculating Geographic Range from Occurrence Data. R Package version 0.1.0. https://CRAN.R-project.org/package=GeoRange

Jablonksi, D. 2005. Mass extinctions and macroevolution. Paleobiology 31:192-210.

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New Data on Titanichthys At Last

Since the last time I posted here I’ve managed to have two new papers published. One in Paleobiology on graptolite extinction risk (Boyle et al. 2017), which I’ll summarize in another post, and one in the Journal of Paleontology (Boyle & Ryan 2017) on the placoderm Titanichthys. The work on Titanichthys was part of my undergraduate capstone research that started waaaay back in 2010 with Dr. Ryan at the Cleveland Museum casually remarking that a new nearly complete skeleton had just been prepared and somebody needed to describe it. So today I’ll be summarizing the results of that paper and where I’d like to get more done on this taxon in the future.

To start, a little background on Titanichthys. It is an old taxon named in 1885 by John Strong Newberry (an interesting man for a number of reasons worthy of his own post) and also a very large animal. Ballpark estimates are a total length >5 meters, making it larger than its more famous contemporary Dunkleosteus and possibly the largest vertebrate animal that had evolved up to that time. The genus is confined to the latest Devonian (Frasnian?-Fammennian) making it one of the last arthrodire placoderms before the entire group perished at the end of the Devonian. The remains of Titanichthys are the second most common taxon after Dunkleosteus but are commonly isolated and fragmentary making its overall morphology somewhat mysterious. Of the 7 currently recognized species only 3 (T. agassiziT. clarki, and T. termieri) are known from at least partially complete specimens. While the description of T. termieri (Lehman 1956) is pretty good by modern standards the other two well-known species were described in the late 19th or earliest 20th century without many modern morphologic conventions and without designation of a holotype. In fact, the effective “holotype” of T. clarki described by Eastman (1907) is a composite of several individuals and has been partially restored with plaster making interpretation of the figures somewhat dubious.

So prior to this new paper the most recent publication on Titanichthys was over 50 years old and we lacked definitive reference material to work from. The new specimen of Titanichthys (CMNH50319) is unique because it is articulated and nearly complete, only lacking parts of the thoracic shield and the ventral shield (Fig. 1). This has allowed for the first description of five new plates (rostral, postmarginal, postsuborbital, submarginal, and posterior superognthal; see Placoderm primer for plate info) and updated descriptions for every other plate that’s been previously described for the genus, with exception of the anterior dorsal lateral. So now we have a very nice specimen to compare new material to and could start looking at the range of variation in morphology. The posterior superognathal was perhaps the most interesting because it is tiny relative to the lower jaw (inferognathal) especially when compared to other arthrodires. This, along with the animals overall large size, the flattened body shape, and elongated lower jaws without anything resembling teeth are all strongly convergent with large filter-feeding vertebrates that are known today such as the Whale Shark, Basking Shark, and Megamouth Shark as well as the fossil teleost fishes Pachycormids. The suggestion that Titanichthys was a filter-feeder wasn’t a novel idea but the new data does lend a lot more support to this hypothesis which could now be tested explicitly.

Figure 2_2col

Figure 1. Reconstruction of CMNH50319 (Titanichthys cf. clarki) in lateral view. Lightly shaded regions are portions of plates that are overlapped. Dark shaded regions are empty space. IG = Inferognathal. Scale Bar = 10cm.

One other important feature we were able to sort out from this specimen was the orientation of inferognathal, which has a deep groove and an anterior tip that bends noticeably from the rest of the jaw. Originally, the groove was thought to be the dorsal surface and to have held tooth plates, making the anterior tip projecting dorsally as well. However, Dunkle and Bungart (1942) presented evidence that the groove faced ventrally making the anterior tip project ventrally as well. When Lehman (1956) described T. termieri he favored the original orientation. Because CMNH50319 had the left inferognathal preserved and articulated with the cheek shield we can now definitively say that the Dunkle and Bungart’s hypothesis is correct. That ventrally projecting tip is odd among arthrodires and can be very strongly developed (Fig. 2) based on observations in the Cleveland Musueum collections. This ventral curve makes the most sense, in my opinion, as an adaptation to increase gape size for filter-feeding.

Tusk Jaw

Figure 2. Reconstruction of undescribed left inferognathal of Titanichthys from the Cleveland Museum of Natural History showing the extreme condition of the ventrally projecting anterior tip. I refer to this as the tusk morph.

Despite all the anatomical detail we were able to report, when it came to assigning CMNH50319 to a particular species we ran into a problem. It had a mix of features from the well-known species and because all the species are poorly known (sample size of 1 or 2) we don’t really have any idea whether those differences are variable within or between species. We did have the inferognathal which is the easiest way to distinguish between T. agassizi and T. clarki, CMNH 50319 was definitively closer to the T. clarki form (it’s worth noting that the inferognathal of T. termieri is not known). So in the end we decided to classify CMNH50319 as Titanichthys cf. clarki, the cf. stands for confers and means close to. We probably could have just called it T. clarki without any complaints but I thought that would mask the uncertainty and variation within the genus.

We were able to perform a phylogenetic analysis with the specimen expanding on previous analyses (Carr 1991, Trinajstic & Dennis-Bryan 2009, Carr & Hlavin 2010,  Zhu & Zhu 2013, and Zhu et al. 2015). We added CMNH50319, T. agassiziBungartius perissus, and Tafilalichthys lavocati to the analysis with 121 characters. The resulting consensus tree (Fig. 3) is not very robust in all honesty. Too many taxa for the number of characters and A LOT of missing data. However, Titanichthys was recovered as a basal aspinothoracid in a monophyletic clade with Tafilalichthys and Bungartius. It will be interesting to see if that clade holds up in the long run because Tafilalichthys and Bungartius have both been associated with taxa that have crushing dentition. That would be a lot of variation in jaw morphology within a single group. I’m convinced the key to resolving arthrodire relationships are the Wildungen taxa from west Germany that seem perfectly placed in time and space to bridge the phylogenetic gap that currently exist.

Phylogeny

Figure 3. Strict consensus of 2769 trees from a PAUP analyis.

Looking ahead to more research in this area several questions are clear. First, we can explicitly test the hypothesis that Titanichthys was a filter-feeder. Second, I gleaned over the geographic distribution of the species but as of right now there were 5! species of Titanichthys coexisting in the Appalachian Basin of North America. For giant filter-feeding organisms that seems incredibly unlikely to me and I suspect that most of the species should actually be synonomized. Looking through the Cleveland Museum collections for this research revealed a large amount of variation in Titanichthys jaws and I wouldn’t be surprised if the different morphs grade into one another or are ontogenetic. There’s plenty of material to work with to explore this project and I’d like to get to it sometime in the future, but if somebody beats me to it I’d be happy just to know that it’s being worked on.

References

Boyle, J. & M.J. Ryan, 2017, New Information on Titanichthys (Placodermi, Arthodira) from the Cleveland Shale (Upper Devonian) of Ohio, USA. Journal of Paleontology, v. 91, p. 318-336.

Carr, R.K., 1991, Reanalysis of Heintzichthys gouldii, an aspinothoracid arthrodire: Zoological Journal of the Linnean Society, v. 103, p. 349–390.

Carr, R.K., and Hlavin, W.J., 2010, Two new species of Dunkleosteus Lehman, 1956, from the Ohio Shale Formation (U.S.A., Famennian) and the Kettle Point Formation (Canada, upper Devonian) and a cladistic analysis of the Eubrachythoraci (Placodermi, Arthrodira): Zoological Journal of the Linnean Society, v. 159, p. 195–222.

Dunkle, D.H., and Bungart, P.A., 1942, The infero-gnathal plates of Titanichthys: Scientific Publications of the Cleveland Museum of Natural History, v. 8, p. 49–59.

Eastman, C.R., 1907, Devonic fishes of the New York formations: New York State Museum Memoir, v. 10, p. 1–235.

Lehman, J.-P., 1956, Les Arthrodires du Dévonien superieur du Tafilalet (sud Marocain): Notes et Mémoires du Service Géologique du Maroc, v. 129, p. 1–114.

Trinajstic, K., and Dennis-Bryan, K., 2009, Phenotypic plasticity, polymorphism and phylogeny within placoderms: Acta Zoologica, v. 90, p. 83–102.

Zhu, Y.-A., and Zhu, M., 2013, A redescription of Kiangyousteus yohii (Arthrodira: Eubrachythoraci) from the Middle Devonian of China, with remarks on the systematics of the Eubrachythoraci: Zoological Journal of the Linnean Society, v. 169, p. 798–819.

Zhu, Y.-A., Zhu, M., and Wang, J,-Q., 2015, Redescription of Yinosteus major (Arthrodira: Heterostiidae) from the Lower Devonian of China, and the interrelationships of Brachythoraci: Zoological Journal of the Linnean Society, v. 176, p. 806–834.