Saturday, October 9, 2010

Kondrashov and Cladistics

            One area of research in Dr. Kondrashov's lab is the phylogenetic reconstruction and the systematics of various animal fauna. Being a paleontologist by training, Dr. Kondrashov is not only interested in the phylogenies of extant or living animals, he is also interested in the phylogenies of extinct animals and uses them to help us understand how the modern animals came to be. One of his recent papers describes a fossil found on an expedition to New Mexico of a Tetraclaenodon. Tetraclaenodon is the most primitive genus of the family Phenacodontidae, and as such it is paramount to the phylogenetic reconstruction of the family. As a Paleontologist, Dr. Kondrashov uses anatomy to infer relationships and to properly classify living and extinct animals (Kondrashov and Lucas, submitted 2010). Much of what I did in this lab rotation was learn anatomy and the methods and rational of morphological based phylogenetic reconstruction.

          Sense the onset of evolutionary theory, specifically the idea that animals are descended from ancestral populations, scientists have been interested in reconstructing the one true evolutionary history of all life. The difficult part is that evolution happened in the past, and as such, what truly happened must be inferred by evidence. Similar to a crime scene investigator, evolutionary biologists use clues or evidence that gives away what actually happened. The techniques for doing this are both interesting and technical.

            The branch of science interested in the diversification of life and the relationships among living things is called Systematics. Methodology in systematics in the 1960's began to change a with the advent of Phylogenetic Systematics in the 1960's by an German entomologist Willi Hennig. Phylogenetic Systematics was later coined Cladistics and is concerned with grouping animals based on their evolutionary history. Cladistics utilizes specific methodology to remove the subjectivity of its predecessors, namely Phenetics, and also to infer the most parsimonious phylogeny. Basically, they create a character matrix which logs character states among different taxa of interest, then use computers to analyze the matrix and group the animals based on the number of similarities shared between taxa. This helps remove investigator bias and makes the methodology more transparent. Dr. Kondrashov used Cladistics in his Tetraclaenodon paper, and will be the method used in my project in his lab.

            The difference between Cladistics and Phenetics is demonstrated by the examination of three groups of animals namely Lepidosaurs (snakes, lizards, etc), Crocodilians, and Birds. Overall, Crocodilians seem to have more in common with Lepidosaurs than Birds. Thus in phenetics, they and other similar organisms are grouped within the Reptiles. Phylogenetic systematists have come to a different conclusion however. Studies employing cladistic analysis on these and other similar animals reveal that Crocodilians and Birds are more closely related than both are to Lepidosaurs (Benton, 1985). This is interesting because Crocodilians and Birds seem like very different animals.

          The rationale behind grouping these seemingly dissimilar groups together is that they share many derived characters or synapomorphies that are thought to have originated in their common ancestor. These animals share an antorbital fenestration, an orbit that is shaped like an inverted triangle, and a muscular gizzard (Hickman et al. 2006). Birds and Crocodilians are thus grouped together under the name Archosauria. Archosaurs share common traits with Lepidosaurs as well, but the common ancestor connecting them with Archosaurs is earlier in history than the Archosaurian common ancestor and as such, Birds and Crocodilians are more closely related to each other than either is related to Lepidosaurs.

           Cladistics is not only reserved for morphological studies. Cladistics is well suited for molecular analysis of nucleic acids or amino acid sequences in order to infer phylogenies. Cladistic analysis will reveal shared derived molecular anomalies and group organisms based on nucleic acid or amino acid sequence similarity. This has become much more prominent with the increase in popularity of molecular biology and computer assisted cladogenesis.

            Dr. Kondrashov had an idea for a project when I arrived. The relationship between major groups of vertebrates are quite resolved with both molecular and morphological data (Janvier 1997), but the relationships of animals within those major groups is sometimes not as resolved. The relationship of Mammals to the other major vertebrate groups (“fishes,” Amphibians, “reptiles” and Birds) is not hotly debated. Even the three subgroups of Mammals namely Monotremes, Marsupials, and Placentals, are highly resolved. However, their have been mixed results in finding the Placental tree root meaning the most basal or ancient group that is the sister taxa to all other Placentals, and also the interrelationships between the various orders within Mammalia.

          I began by reviewing the literature on Placental Mammal phylogenetics. There have been many recent molecular studies on the infraordial relationships of Mammals (Delsuc et al. 2001, Delsuc et al. 2002, Hallström et al. 2007, Wildman et al. 2007, and Murphy et al. 2007) all with differing trees and roots based on the methods and nucleic acid sequences used. There have also been several morphological studies done on the various Placental mammal groups (Fu-Guo et al. 2001, Asher et al. 2003, Asher 2007, and Asher et al. 2008) with similar results. Our project is to study the relationships of the Xenarthrans using morphological data. We will also include several extinct animals that represent a better picture of Xenarthran diversity.

           Asher 2007 provided an online database of the morphological characters used in his study ( This is extremely helpful because it provides me many meaningful characters (potential synapomorphies) that I could include in my project. I spent much of my time in Dr. Kondrashov's lab learning the anatomy of all of these characters (there are 185 characters with several character states each). I will also have to learn the characters specifically in the animals that I will include in my project.

Asher, R.J.; et al. Relationships of Endemic Aftican Mammals and Their Fossil Relatives Based on Morphologiccal and Molecular Evidence.” Journal of Mammalian Evolution. 10 (2003) 131-142.
Asher, R.J. “A databast of Morphological Characters and a Combined-Data Reanalysis of Placental Mammal Phylogeny. BMC Evolutionary Biology. 7 (2007) 108.
Asher, R.J.; et al. Morphology, Paleontology, and Placental Mammal Phylogeny.” Systematic Biology. 57 (2008) 2:311-317.
Benton, M.J. “Classification and Phylogeny of the Diapsid Reptiles.” Zoological Journal of the Linnean Society. 84 (1985), 2:97-164.
Delsuc, F.; et al. “The Evolution of Armadillos, Anteaters, and Sloths Depicted by Nuclear and Mitochondraial Phylogenies” Implication For the Status of the Enigmantic Fossil Eurotamandua.” Proceding of the Royal Society of London. 268 (2001) :1605-1615.
Delsuc, F.; et al. “Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling of the Placental Tree Rooting.” Molecular Biology and Evolution. 19 (2002) 10:1656-1671.
Fu-Guo, R.L.; et al. Molecular and Morphological Supertrees for Eutherian (Placental) Mammals.” Science. 291 (2001) 1786-1789.
Hickman, C.P.; et al. Integrated Principles of Zoology, Thirteenth Edition. New York: McGraw Hill, 2006.
Hallstrom, B.M.; et al. Phylogenomic Data Analyses Provide Evidence that Zenarthra and Afrotheria Are Sister Groups.” Molecular Biology and Evolution. 24 (2007) 9:2059-2068.
Janvier, Philippe. Vertebrata. Animals with backbones. Version 01 January 1997 . <> in The Tree of Life Web Project,<>
Kondrashov, P; Lucas, S. “A Nearly Complete Skeleton Of Tetraclaenodon (Mammalia, Phenacodontidae) From the Early Paleocene of New Mexico: Morpho-Functiona Analysis.” Journal of Vertebrate Paleontology. Submitted June 29 2010.
Murphy, W.J.; et al. Using Genomic Data to UnRavel the Root of the Placental Mammal Phylogeny.” Genome Research. 17 (2007):413- 421.
Wildman, D.E.; et al. Genomics, biogeography, and the Diversification of Placental Mammals.” Procedings of the National Academies of Sciences of the USA. 104 (2007) 36:14395-14400.


1 comment:

  1. Xenarthrans is a beautiful name for an armadillo. It sounds like it should be a Greek goddess with the Zena prefix, but I can also hear the arthropod sound in there and I do think armadillos are very similar to arthropods. I have hiked many trails with these creatures in the Texas hill country and the Edwards plateau. Too cool you are studying the entire group to sleuth out answers about evolutionary origins. Hope I am not slaughtering your sophisticated anatomical analysis... keep it up!