Our Writer of the Week for our week centered around scientific writing is
Andrew Hallstrom ’22.
About him: “I am a junior Physics major with an Astrophysics concentration and minors in Biology and Mathematics. I’m from the small town of Roscoe, IL, and enjoy listening to music, playing basketball, and hanging out with friends. At Carthage, I am the president of Delta Upsilon social fraternity, am a member of the WSGC Collegiate Rocket Launch team, and participate in research about gravitropism in plants.”
His paper is titled “Cladistic Analysis Showing Recovery of Archaea + Bacteria, Archaeplastida, and Eukarya with flagella from RNA Using PAUP” and describes the lab he carried out that analyzed the evolutionary relationships between different organisms.
Our fellows found it very readable and engaging.
Ashley G: “The ideas are complex, yet presented in a way that is easy to follow.”
Jackie: “It is technically very well-written and has good organization, and the content is interesting and well-explained.”
Andrew said of his paper, “This piece of writing is a lab report for BIO 1120: Organisms, Populations, and Systems. Titled ‘Cladistic Analysis Showing Recovery of Archaea + Bacteria, Archaeplastida, and Eukarya with flagella from RNA Using PAUP’, the report focuses on the relationships between 71 taxa, or groups of organisms (I know the name isn’t too catchy, but that’s the format that our professor wanted our title to be in). The objective of the lab was to recover sister groups; that is, groups that are evolutionarily close to each other. This was done using the online programs Mesquite and PAUP, along with characters, or traits, that set the taxa apart. This lab was interesting to me because we got to focus on a lot of different types of organisms that I had never heard of, and it helped me understand our evolutionary history.”
Cladistic Analysis Showing Recovery of Archaea + Bacteria, Archaeplastida, and Eukarya with flagella from RNA Using PAUP
Through the use of Morris’ How Life Works, Mesquite, and PAUP, a cladogram of 71 taxa and 110 characters was recovered. 16 sister groups were identifiable. Mesquite was used to construct a character matrix, and the matrix was then input into PAUP , where a strict consensus tree and a described tree were recovered. Although there were clear errors in the analysis due to incorrect input of data, the main sister groups of Archaea + Bacteria, Archaeplastida (Land Plants + Green Algae), and Eukarya with flagella (Choanoflagellates + Animalia) were identified, with especially detailed sister groups evolved from the latter two, such as Fungi, Land Plants, Vertebrates, Ecdysozoa, and Arthropoda. These clades account for the majority of the used taxa. The described tree recovered from PAUP showed differences from the strict consensus tree as well as data from How Life Works. These differences included the location of Fungi within the tree as well as the relations between Alveolata and Stramenopila. More specifically, the strict consensus tree placed Fungi as a sister group of Archaeplastida, whereas Fungi was shown as a sister group to Animalia in How Life Works. Fungi, along with Stramenopila and Alveolata, where shown in the strict consensus tree to have evolved at the same time as Archaea + Bacteria. In How Life Works, Archaea + Bacteria evolves before Stramenopila and Alveolata, and are not a sister group with those two.
The purpose of this lab was to find the sister relationships between various clades using the programs Mesquite and PAUP. This is fundamental biology because evolution is one of the most basic foundations in the field of biology; most other theories regarding the origins of life on Earth are based off Darwin’s theory of evolution. Furthermore, this lab was an exercise in fundamental biology since characters were used to find ancestral connections between the different taxa. The objective of the lab was to determine which groups were sister groups. This objective was achieved by using How Life Works (Morris et al., 2019) to identify taxa and characters. These taxa and characters were input into a state matrix and then a character matrix on the program Mesquite (Maddison & Maddison, 2018). A strict consensus tree (Figure 1) and a described tree (Figure 2) were then derived by PAUP (Swofford, 1997) showing relationships between the different taxa and clades. A redrafted tree (Figure 3) was then constructed based on the described tree (Figure 2) to show more information about the sister groups recovered. The goal of this analysis is to look deeper into these previously stated relationships.
Methods and Materials
For this lab, 71 taxa were used (Appendix 1). RNA was identified as the outgroup, with the remaining 71 taxa being the ingroup (Figure 1). To find the relationships between these taxa, 86 characters were identified (Appendix 2). A character matrix was compiled in the program Mesquite (Maddison & Maddison, 2018) to show the relations between the taxa and characters (Appendix 1). Originally, 87 taxa were used, but 16 taxa (Bacteria, Eukarya, Opisthokonta, Archaeplastida, Bilateria, Deuterostomia, Ecdysozoa, Lophotrocozoa, Arthropoda, Vertebrates, Mammals, Placental Mammals, Humans, and Homo sapiens) were deleted from the matrix to eliminate redundancy during the analysis. After the matrices were constructed using Mesquite (Maddison & Maddison, 2018), the results were input into the program PAUP (Swofford, 1997).
The PAUP analysis recovered 2184 trees, from which a strict consensus tree was
produced (Figure 1). This strict consensus tree showed the members of the clades of Eukarya, Archaea + Bacteria, and Archaeplastida sharing a common ancestor in RNA. Looking at the descendants of Archaeplastida and Vertebrates, it is shown that the trees in How Life Works (Morris et al., 2019) were supported by this analysis. However, the described tree returned by PAUP (Figure 2) followed Morris’ examples less accurately, with only some differences between the two (Morris et al., 2019). The clades that were presented in How Life Works (Morris et al., 2019) were not all accurately recovered. Ecdysozoa was not accurately recovered, and Fungi was recovered as a sister group of Archaeplastida rather than a sister group of Opisthokonta. The tree had a length of 151, and a consistency index (CI) of 0.7550. The following clades were recovered.
The first clade chronologically is cellular life. This contains all taxa from the ingroup. Cellular life evolved 3.5 billion years ago (Morris et al., 2019), and is characterized by a cell membrane, organelles, ester-linked lipids, histone proteins, and introns.
From cellular life, one path of the tree leads to the sister group of Bacteria + Archaea. These taxa evolved 3.5 billion years ago (Morris et al., 2019). Characteristics include growth at 80 degrees Celsius, operons, nitrogen fixation, chemoautotrophy, and thin cell walls. Archaea split off, characterized by ester-linked lipids and methanogenesis.
Continuing down the tree opposite of Archaea and Bacteria, Eukarya evolved 2.7 billion years ago, and were characterized by organelles, a ribosome size of 80S, and introns (Morris et al., 2019). The clade of Eukarya involve the sister groups Amoebozoa, photosynthetic Eukarya, and Eukarya with flagella.
From the photosynthetic group, Archaeplastida evolved. Archaeplastida evolved about one billion years ago (Morris et al., 2019), and are defined by two-membrane chloroplasts, multicellularity, and multiple tissues. From Archaeplastida, land plants evolved 500 million years ago (Morris et al., 2019). Land plants have a diploid generation. Vascular plants evolved from land plants 425 million years ago (Morris et al., 2019). These plants all have xylem and phloem. From the vascular plants is the seed plants. As the name suggests, seed plants evolved to produce seeds and pollen for sexual reproduction. This clade split from the other vascular plants about 350 million years ago (Morris et al., 2019).
Fungi evolved around one billion years ago (Morris et al., 2019). Fungi are characterized by chitin in their cell walls. From Fungi, the clade of Dikarya was recovered. Having evolved 50 million years ago, Dikarya are characterized by regular septa and ectomycorrhizae (Morris et al., 2019).
From Eukarya with flagella, Opisthokanta evolved around 800 million years ago (Morris et al., 2019). They are characterized by multicellularity and blastula. From this group, three more sister groups were recovered: Lophotrochozoa, Arthropoda, and Deuterostomia. Lophotrochozoa are defined by spiral cleavage early in their lives. They evolved around 550 million years ago (Morris et al., 2019). Arthropoda evolved around 500 million years ago (Morris et al., 2019). All arthropods have jointed legs for walking, chitin, and a jaw. Deuterostomia have cilia, a blastopore that forms into a mouth, and specialized respiratory systems. They evolved about 520 million years ago (Morris et al., 2019). From Deuterostomia, Vertebrates evolved. This evolution took place around 500 million years ago (Morris et al., 2019). Vertebrates all have vertebrae, as the name suggests.
The most recent clade recovered by the PAUP analysis was Mammals. Mammals evolved from Vertebrates a little less than 200 million years ago (Morris et al., 2019). Mammals are defined by mammary glands and hair, and includes the clade of Humans, where the described tree ends (Figure 2).
It is evident that there are clear differences between the phylogeny in Morris’ textbook and the results of this lab. For example, Fungi should not be included in Archaeplastida, and Ecdysozoa never branched off (Figure 2). These differences could be due to errors in entering character states for each of the taxa, as well as not including enough characters to differentiate the taxa.
Based on the described tree, the most important events that occurred throughout the evolutionary history of the taxa are as follows: Archaea and Bacteria evolved first, followed by Archaeplastida and other Eukarya. With Archaeplastida, the evolution of land plants is shown, and within Eukarya, Arthropoda, Vertebrates, and Lophotrochozoa are recovered. It is evident that this tree is not fully accurate. Some taxa do not appear where they do in How Life Works (Morris et al., 2019), such as Fungi, Stramenopila, and Alveolata. Everything that was recovered is fundamental biology, however. The most prevalent theory of evolution is that life arose from single celled organisms, such as Archaea and Bacteria. This is proven by the described tree (Figure 2).
The lineage of plants is concise and clear: land plants lead to vascular plants and eventually seed plants. The lineage of single-celled organisms, including Archaea + Bacteria, is also straightforward. The derivation of gram-negative bacteria from ancestral bacteria can also be seen in How Life Works (Morris et al., 2019). The development of the clade of Animalia is also very clear. The most change was seen when the clade of Archaea + Bacteria split from cellular life (six synapomorphies), and the least change was within the evolutions of the different Vertebrates (one synapomorphy).
Maddison, D.R., and Maddison, W.P.. Mesquite. 2018.
Morris, J., Hartl, D. L., Knoll, A. H., Lue, R., & Michael, M. (2019). Biology: How Life Works, Third Edition. New York, NY: W.H. Freeman and Company.
Swofford, David. PAUP. 1997.
To see the Figures and Appendices for this paper, click here.