Why can't we all just get along?: Morphological vs. Molecular Data

Hello everyone, staying on top of things in a timely manner is far harder then I care to admit. Still, here is a new post. These may still be somewhat infrequent until I can finish up my thesis, or a least the first draft of it. But once February hits, perhaps these will be more on track. Here's hoping.....

http://txtwriter.com/Backgrounders/Dinosaurs/dinoBG2.html

So, for those of you who have looked into phylogenies, especially those concerning modern taxonomic groups and modern genera in particular, you may have run into some problems (or you may not have, I don't actually know for sure). I will focus on a specific case, but this will not be the end.
 




Many people are aware of phylogenies, cladograms, and the concept of systematics in general. These are ways to convey the relationships between organisms and help (or possibly help) show evolution through time. These are commonly used in biology and paleontology today. These two fields don't always use the same data sets though. This is not really surprising, since biologists working with modern taxa have the ability to get far more data, while paleontologists commonly only have morphological characters from the fossils they can find. While biologists commonly have several types of data they can use to acquire phylogenies, a relatively common one is molecular data. And this makes sense, DNA should be able to be used for discussing and discovering the relationships of living things to each other.

http://www.onlpharmacy.com/blog/tag/genomic-information

Sure enough, phylogenies based on molecular data are quite common. A simple search for "molecular phylogeny" in Google Scholar gives >326,000 results. While these can deal with anything from bacteria, to plants to animals, to distinct parts of animals. These have allowed people to discover far more information about relationships of living things. The concept is simple enough, use the same basic thing to compare, say a certain nucleotide or protein, pick your set of organisms with one or more outgroups, align them, then compare them. As a note, you want to have roughly the same numbers for each individual you use. So, say you investigate the cytochrome b protein in felids, you would want the total number of proteins in each taxon to be roughly, say all around 200 total aa proteins (or whichever number you decide upon).

After aligning all of them and running them through a program like PAUP, you will get at least one cladogram. It may look something like this:

Stephens and Wiens 2003, fig. 3

The above figure is figure 3 from Stephens and Wiens (2003). It shows two molecular phylogenies, one as maximum parsimony (a) and the bottom as maximum likelihood (b). I won't be getting into the difference between the two at the moment, just realize they are two slightly different ways of analyzing the same data. The two phylogenies actually do combine three separate data sets though and combine them. They both use cytochrome b, 16S and ND4 data sets.

At first glance, it seems that these do a very good job of agreeing with the known taxonomy presented by the different genera. The only problem is that Clemmys is strongly split at the bottom of the phylogenies. This was cleaned up after this paper was published, however, with the Western pond turtle (Actinemys) and the wood turtle and bog turtle (Glyptemys) being placed in different genera.

Actinemys marmota (left) Glyptemys muhlenbergii (top), Glyptemys insculpta (bottom)

 So, in just looking at the molecular data, the family Stephens and Wiens (2003) were investigating seems to be pretty well off. But they didn't leave it to just that data. They also looked into the morphological data as well:

Figures 4 and 5 from Stephens and Wiens (2003)

Graptemys flavimaculata

These two figures above [figs 4 and 5 from Stephens and Wiens (2003)] show the authors' results on there morphological data alone. They did use soft tissue, osteological, morphometric, and statistical data as part of this set. The use of any of those sets can be debated, and has by some people. They also use two ways of attempting to scale the data so that weighting would be, presumably, the same. I won't get into those here, but be aware of them and that they are not agreed upon fully. What can be easily seen is that the two phylogenies above do not agree with each other. The relationships shown are not the same. In the phylogeny on the left, Pseudemys comes out as the most derived member, while the one on the right has Graptemys in the same position.

Trachemys scripta elegans

I would like to focus on Trachemys though. The slider turtles are the subject of my Master's thesis at the moment, and have been the topic of much debate for quite a while now. Without getting too detailed at the moment, it is apparent that many researchers have been well aware of the problems, but no one has taken it upon themselves to completely clear it up. Dale Jackson did some work on the group in the 1970's and 1980's, but their is still far too little known about them. What can be seen is that the members of Trachemys in the phylogenies above does not come out as a cohesive or monophyletic group. Not only the genus, but, many times, the supposed species (with their respective subspecies) don't group together well either. In these instances, Trachemys comes out as either paraphyletic or polyphyletic. It can even be seen in the phylogeny on the right that the Pseudemys group is well nested within Trachemys.

This is a bit disturbing to someone researching the group. What exactly is going on? One key aspect to keep in mind is that convergence due to similar lifestyles can be a big problem. If different taxa have evolved the same or similar features to do the same things, they may be seen as more closely related then they truly are. This depends on the characters and features that people use to make their phylogenies though. The hope is that, with enough characters and features being used, the true relationships will come to light. If that is the case or not is not actually known at the moment.

Paleontologists only have the luxury of morphological data sets. Perhaps one day we will get some DNA from a dinosaur or other long extinct species, but that is not so today. They use what they can, and come up with phylogenies and relationships based on that data alone. It has been said by some researchers, including John Wiens on numerous occasions, that combining the molecular and morphological data sets is a good idea. The idea being that they will strengthen each other, assuming that they are both working towards the same end (correct?) phylogeny. It was suggested to me that, even working with fossils and modern taxa, and even only having molecular data for the modern taxa, that combining the data sets would be recommended and should strengthen all the relationships in a phylogeny of fossil and modern taxa. Stephens and Wiens (2003) did this as well with their modern taxa, combining all their data sets with the following phylogeny:

Figure 7 from Stephens and Wiens (2003)

Malaclemys terrapin

In the figure above, which shows all taxa in their study, Trachemys first appears to fall out all together. All Trachemys species appear within a "group", all their names above or below each other, with no other nested genera present. If you look more closely though, you will see that Trachemys is still not monophyletic. In this instance, they should either be split apart into 5 (yes 5!) different genera, or have other genera combined as Trachemys. This seems somewhat crazy, since most researchers have felt that the group was either fairly well set, or that they should be combined with Pseudemys and/or Chrysemys. In fact, with this grouping, it would be Graptemys and Malaclemys that should be grouped with Trachemys to make it a monophyletic group. As a note, I DON'T believe that the idea of subgenera is a good idea and/or the answer.

They also had a second phylogeny which only took into account the taxa with complete data sets (Stephens and Wiens, 2003, fig. 8), which is to the right here-------------------------------->

These groupings seem to become far nicer and follow known taxonomic groups. It is of note, though, that only a single Trachemys species is present in this table. So, is it Trachemys alone that is causing all these problems?







I am not so sure of that. It makes more sense for it to be a problem with a number of taxa within the Deirochelyinae, although Trachemys may be the biggest trouble-maker. I believe that convergence is one of the biggest problems here. Many of these turtles live in similar environments and do similar things. Because of this, they have developed many of the same features. A key area to look at may simply be what features are being used for these phylogenies. Another key area could be that more molecular data needs to come to light on this group in general.

Regardless, I have talked with Dr. Jacques Gauthier, who has informed me that this kind of concept, where the molecular and morphological data do not agree, is a relatively common occurrence. Not just with this group, or even just turtles, but many groups. This is especially true when dealing with fossils and fossil groups.

The molecular data seen above does not agree with the morphological data. In essence, because they don't agree, they are working against each other. When combining the two different sets, the one with the most data will simply win out. This is not what we are scientists are striving for. We want the two different kinds of data to agree and give us a stronger idea of the true relationships present. Sometimes this does happen and they data sets essentially agree, but all too often that is not the case.

Ray-finned fish evolution from Hurley et al. (2007), image from Dracovenator blog

So, why can't the molecular data and morphological data agree? While I don't know the exact answer, I believe that eventually they will. We just haven't gotten enough of either. We must believe that the true relationships will eventually come to light with enough good data. So keep plugging away, and we will figure these things out. Even if the organisms themselves do not care how they fit in together; Trachemys doesn't care how it relates to the Alligator that may be trying to eat him, many people, myself included, do care.

Trachemys and alligatorid

Look to the Dracovenator blog post titled: Problems in Ray-Finned Evolution to see another case of disagreement with a different group, the ray-finned fishes.


References:

Stephens, P. R. amd J. J., Wiens. 2003. Ecological diversification and phylogeny of emydid turtles. Biological Journal of the Linnean Society 79:577-610.

Hurley, I.A., Lockridge Mueller, R, Dunn, K.A.,Schmidt, Friedman, M., Ho1, R.K., Prince, V.E., Yang, Z., Thomas, M.G. and Coates, M.I. (2007)A new timescale for ray finned fish evolution. Proc. R. Soc. B 274, 489–498 

Cretaceous Turtles of New Mexico Part 1: Here comes the meteor?

Since some of you may be aware that one of my major interests revolve around turtles, both alive and dead, its surprising that its taken me this long to post anything on this amazing group or reptiles. While there are an incredible number of things that can be posted, this will be more of a simple post based around one of my recent papers (Jasinski et al., 2011). From what is known about the San Juan Basin, specifically in New Mexico, these are the last turtles known before the K-T extinction event and the moment in time when the bolide hit the Yucatan.

Glyptodontopelta mimus from Naashoibito Member (Ojo Alamo Formation)

Ojoceratops fowleri

The study itself was on all the fossil vertebrates recovered from the Naashoibito Member of the Ojo Alamo Formation (Jasinski et al., 2011). The fossil vertebrates from this stratigraphic unit have been grouped together in what is called the Alamo Wash local fauna and were originally studied by Lehman (1981), but were in thorough need of revision. There are several key dinosaur taxa within this fauna, including the recently named Ojoraptorsaurus boerei. Other endemic taxa to this fauna include the ankylosaur Glyptodontopelta mimus and the ceratopsid Ojoceratops fowleri. It is also contains the types of Alamosaurus sanjuanensis, the youngest sauropod from North America. Alamosaurus has a number of potential problems though, and I will be touching on those in later posts.

So, the focus of this post is on those lovely creatures how keep their houses on their backs. The turtles from the two underlying formations are under study by Dr. Robert Sullivan and others and the study is currently waiting to come out in an upcoming volume on fossil turtles dedicated to Dr. Eugene Gaffney. So we will hope it comes out sooner rather than later. The turtles from the Naashoibito Member are vastly understudied and little attention has been paid to them. Much of this is because most material is very fragmentary, and there has been little there that would even qualify as a potential holotype for a turtle species.

reconstructed Basilemys, similar to Basilemys nobilis

Even so, two turtle species have been named from this unit. The first, called Basilemys nobilis, was named by Hay (1911) based on several carapace and plastron fragments. Basilemys is a member of the Nanhsiungchelyidae, and represents the only definitive terrestrial turtle from this turtle fauna. The forthcoming study by Sullivan et al. came to the conclusion that B. nobilis was a nomen dubium. While a recently recovered specimen may yet prove that a legitimate species of Basilemys is present in the Naashoibito Member, the holotype of B. nobilis will still probably be taxonomically undiagnostic.

reconstructed shell of Adocus

The second holotype, named Adocus vigoratus by Hay (1911), is based on several carapace fragments. Adocus is currently part of the family Adocidae, although at one point it was considered in the same family as Basilemys. Being an aquatic species, it probably inhabited a familiar niche throughout the late Cretaceous and into the Paleocene. Jasinski et al. (2011) felt that the type specimen of A. vigoratus was undiagnostic though, and considered it a nomen dubium, although it does represent an adocid in the fauna.

Kinosternon subrubrum, close living relative of Hoplochelys

Recent studies on Compsemys (Knauss et al., 2011) and Hoplochelys (Lyson and Joyce, 2011), have revealed many synonymies for these two previously ill-studied turtles. While the specimens of the ?pleurosternid Compsemys and the kinosternoid Hoplochelys are generally quite fragmentary in this fauna, both have been referred to specific species. The ?pleurosternid is now called Compsemys victa and all North American Compsemys are thought to represent one species. The kinosternoid Hoplochelys has now been referred to the species H. clark, as has all Cretaceous specimens of Hoplochelys. Both turtles would have represented small aquatic species. Compsemys was a small gracile turtle with a number of distinct places on the shell with small and distinct bumps and small ridges.

Neurankylus (a baenid) showing color spots found on specimen from Paleocene in San Juan Basin

Boremys (Baenidae)

The Baenidae are a group of aquatic turtles well-represented throughout the Cretaceous and Paleocene. They come in a variety of sizes, but are commonly quite robust for water turtles. Considering the overall number of turtle fossils recovered from the Naashoibito Member, baenids are some of the most common. Even with the generally large number of turtle fossils, none have been identified to a given genus yet. This is because most are very fragmentary or undiagnostic.

Plastomenus, similar to a turtle found in Naashoibito Member

The Trionychidae are a group of aquatic turtles today commonly called soft-shell turtles. These turtles have been around since the Cretaceous and continue today around the world. Surface texture makes shell fragments easy to identify to the species, and one or more new species may yet be named from the trionychid material already collected from the Naashoibito Member. The only turtle skull material from this member is also from a trionychid, identified by Jasinski et al. (2011) as the right parietal of a large trionychid called Plastomenus.

A modern trionychid, Apalone spinifera, the spiny softshell turtle

Various other fragments of turtles have been recovered as well, but these are too fragmentary to assign to any specific family of turtles. I realize that this was a relatively small post, but I wanted to put this out there for the future. This is a small look at the last turtles known from the Cretaceous in this region of the world. While the age of this member has been debated for years, the two generalized camps range from either an early Maastrichtian age (~68 Mya) or later Maastrichtian (~66 Mya). I am currently working on a study into how the turtle fauna of the San Juan Basin across the K-T Boundary, which is leading to some interesting conclusions. I won't go into to much detail, but if you are going to SVP this year in Las Vegas, hopefully you will seek me out and ask me about them.

REFERENCES CITED

Hay, O. P. 1911. Descriptions of eight new species of fossil turtles from the west of the one hundredth meridian. Proceedings of the United States National Museum 38:307-325.

Jasinski, S. E., R. M. Sullivan and S. G. Lucas. 2011. Taxonomic composition of the Alamo Wash local fauna from the upper Cretaceous Ojo Alamo Formation (Naashoibito Member), San Juan Basin, New Mexico. New Mexico Museum of Natural History and Science Bulletin 53:216-271.

Knauss, G. E., W. G. Joyce, T. R. Lyson, D. Pearson. 2011. A new kinosternoid from the Late Cretaceous Hell Creek Formation of North Dakota and Montana and the origin of Dermatemys mawii lineage. Paläontologische Zeitschrift 85:125-142.

Lehman, T. M. 1981. The Alamo Wash local fauna: A new look at the old Ojo Alamo fauna; pp. 189-221 in Lucas, S. G. (ed.), Advances in San Juan Basin paleontology. University of New Mexico Press, Albuquerque. 

Lyson, T. R., and W. G. Joyce. 2011. Cranial anatomy and phylogenetic placement of the enigmatic turtle Compsemys victa Leidy, 1856. Journal of Paleontology 85:789-801.

Sullivan, R. M., S. E. Jasinski, and S. G. Lucas. in press. Re-assessment of Late Campanian (Kirtlandian) turtles from the Upper Cretaceous Fruitland and Kirtland formations, San Juan Basin, New Mexico; in Brinkman, D., J. Gardner, and P. A. Holroyd. (eds.). Morphology and evolution of turtles. Springer Press, Dordrecht.