Molecular phylogeny of an elephant-like species

A molecular phylogeny of the extinct South American gomphothere through collagen sequence analysis

By: Michael Buckley, Omar P. Recabarren, Craig Lawless, Nuria Garcia, Mario Pino

Summarized by: Stormie Gosdoski a student at the University of South Florida. She will be receiving her Bachelor of Science in Geology this December, 2020. After school she plans to join the scientific community and put her degree to good use. 

Data: Phylogenetic trees are created to determine the closest possible relationships between species, like a family tree. The phylogenetic tree containing gomphotheres, a group related to modern elephants, was created by analyzing molecular differences across species and determine the relationships between gomphotheres and true elephants and mammoths. One of the most informative ancient biomolecules that scientists can use for this type of study is collagen, which is the most abundant protein in bones and teeth. 

The scientists sampled four different gomphothere fossils belonging to a genus called Notiomastodon from South America. To reduce extraneous variables that could be present in the dataset, all the fossils were taken from the same location: the Pilauco Site in Osorno, Chile. They were also taken from the same layer of sediment. The layers of sediment on Earth can be read like a book, if no other geologic event has altered their positions. The ability to read each layer like a book gives scientists the ability to date the specimens; 13,650 ± 70 years ago to 12,372 ± 42 years ago. The fossils collected from this site included two root molars, a piece of rib, and a skull fragment.

Methods: The bones had fragments removed from them using a diamond-tip Dremel drill. They were then demineralized in hydrochloric acid (meaning, the scientists removed the minerals from the bones). The collagen was extracted from the solution. It was analyzed by a machine called a Matrix Assisted Laser Desorption Ionization Mass Spectrometry Time-of-Flight Mass Spectrometry (MALDI-ToF-MS). This type of equipment is used specifically to find the protein fingerprint of cells (which, just like our fingerprints, are unique to specific groups). The data collected from these methods were compared and searched for on the Swiss-Prot database for any potential matches to the primary protein sequences that are present in the collected data. This database is a protein sequence database. A potential match in the database would mean the species are more closely related. Once the analysis was complete, the scientists then performed a phylogenetic analysis of the data collected. Meaning, they compiled this information and ran the phylogenetic analysis using these new specimens and animals belonging to the closely related proboscideans, the group including elephants and mammoths, in the database as well, to determine relationships of the organisms in question.

Results: The protein fingerprint spectra of the four specimens collected in this study compared to the spectra of woolly mammoth and American mastodon was determined to differ from one another. The collagen fingerprints were similar, but there were three variations observed in the data (figure 1). At this point, using parsimony, Bayesian analysis, and maximum likelihood (the three methods of determining evolutionary relationships) a range of phylogenies was generated. This range compared three extinct proboscideans (Mammuthus, Mammut (the American mastodon), and Notiomastodon) and other closely related mammals. The results of these comparisons showed a closer relationship between Notiomastodon and Mammut. Meaning, the South American gomphothere has a close relationship to the American mastodon (figure 2).

Figure 1 This figure is the mass spectrometry of the three species. (Top to bottom) gomphothere (green), mastodon (blue), and woolly mammoth (red). This shows observed peak difference in the spectra between the three species.

Importance: This determination of the relationship between gomphotheres and mastodons can change how scientists interpret the relationships of other species in phylogenetic studies. Are there other relationships that need to be changed? How accurate can the scientific community get with the relationships of species? How does this affect our relationship to other species? How can we use this type of analysis to track our own evolution through time? This relationship is but one small portion of a larger question and we can use this to refine what we already know about ancient and present species.

The Big Picture: As scientists, we cannot rely on what our eyes are seeing to determine the relationships between species. Using molecular analyses can give a better idea of how closely related species are to one another. This type of analysis can also show how elephants have evolved and changed through history. This can give scientists a better understanding of the biology of elephants. Who knows- maybe it could lead to predictions of how the species will evolve in the future?

Figure 2 This is the phylogenetic tree that was generated from the analysis with ancient ancestor Paenungulata at the bottom (yellow) and the branch containing the common ancestor at the focus of the study, Proboscidea (pink). The South American gomphothere (green) is the sister taxon to the American mastodon (blue). It further shows the relationships of the other species. On the left is the geologic time scale, which shows when each species was alive.

Citation: Buckley, M., Recabarren, O. P., Lawless, C., García, N., & Pino, M. (2019). A molecular phylogeny of the extinct South American gomphothere through collagen sequence analysis. Quaternary Science Reviews, 224, 105882.