# Structural Biochemistry/Bioinformatics/Evolution Trees
## History

Early signs of branching evolutionary trees or phylogenetic trees are paleontological charts. This kind of chart was illustrated in Edward Hitchcock's book called the Elementary Geology, which showed the geological relationships between that of plants and animals. However, going way back in time, the whole idea of tree life first started from the ancient notions of a ladder-like progression from the lower to the higher forms of life. An example of a ladder-like progression would be that of the Great Chain of Being.
In addition, a well-known man named Charles Darwin from the 1850s produced one of the first drawings of evolutionary tree in his seminal book called "The Origin of Species". Basically in this book, he showed the importance of evolutionary trees. After many years later, many evolutionary biologists studied the forms of life through the use of tree diagrams to depict evolution. The reason for this is that these types of diagrams prove to be very effective at explaining the concept of how speciation happens through the random splitting of lineages and the idea of adaptive. Overall, for many centuries, many biologists used the tool evolutionary trees as a way to study the idea of life.

## Phylogeny

Evolutionary trees, or Phylogeny, is the formal study of organisms and their evolutionary history with respect to each other. Phylogenetic trees are most commonly used to depict the relationships that exist between species. In particular, they clarify whether certain traits are homologous (found in the common ancestor as a result of divergent evolution) or homoplasy (or sometimes referred to as analogous, a character that is not found in a common ancestor but whose function developed independently in two or more organisms, known as convergent evolution). Evolution Trees are diagrams that show various biological species and their evolutionary relationships. They consist of branches that flow from lower forms of life to the higher forms of life.
Evolutionary trees differ from taxonomy. Whereas taxonomy is an ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences, evolutionary trees involve biological classification and use morphology to show relationships. Phylogeny is shown by evolutionary history using the relationships found by comparing polymeric molecules such as RNA, DNA, or protein of various organisms. The evolutionary pathway is analyzed by the sequence similarity of these polymeric molecules. This is based on the assumption that the similarities of sequence result from having fewer evolutionary divergence than others. The evolutionary tree is constructed by aligning the sequences. The length of the branch is proportional to the amount of amino acid differences between the sequences.
Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters. Comparing nucleic acids or other molecules to infer relationships is a valuable tool for tracing an organism's evolutionary history. The ability of molecular trees to encompass both short and long periods of the time is hinges on the ability of genes to evolve at different rates, even in the same evolutionary lineage. For example, the DNA that codes for rRNA changes relatively slowly, so comparisons of DNA sequences in these genes are useful for investigating relationships between taxa that diverged a long time ago. Interestingly, 99% of the genes in humans and mice are detectably orthologous, and 50% of our genes are orthologous with those of yeast. The hemoglobin B genes in humans and in mice are orthologous. These genes serve similar functions, but their sequences have diverged since the time that humans and mice had a common ancestor.
Evolutionary pathways relating the members of a family of proteins may be deduced by examination of sequence similarity. This approach is based on the notion that sequences that are more similar to one another have had less evolutionary time to diverge than have sequences that are less similar.
Evolutionary trees are used today for DNA hybridization. They are used to determine the percentage difference of genetic material between two similar species. If there is a high resemblance of DNA between the two species, then the species are closely related. If only a small percentage is identical, then they are distant in relationship.

## Construction of a Evolutionary Tree

Each point at which a line in a evolutionary tree branches off is known as a node. A node is a common ancestor to the species that come off that branch. Relationships between species in an evolutionary tree include monophyletic, paraphyletic, and polyphyletic. A monophyletic group is a branch of species which contain a common ancestor and all descendants. Paraphyletic groups consist of a common ancestor but not all its descendants. Polyphyletic groups consist of organisms that do not have a (recent) common ancestor and are usually compared to study similar characters among relatively unrelated organisms.
These nodes are calculated by using a computational phylogenetic program that calculates the genetic distance from multiple sequence alignments. However, there are limitations, primarily not being able to account the actual evolutionary history. While the sequence alignment shows comparatively how related two species are, there is no indication as to how they evolved. Therefore for these the origins of the three domains came from the same ancestor and then branches out to the two distinct groups Eukarya and Prokarya. However, the Archaea branches out of the Eukarya domain, even though they are single-celled.
Evidence for Phylogeny construction: 1. By looking at the fossil record. The problem is that the record is incomplete and only hard structures were preserved. 2. By studying recent species, looking at the shared characters, both homologous and analogous characters, give evidence of evolutionary past.

## Types of Evolutionary Tree

There are many different types of evolutionary trees and each one represents something different. One type of evolutionary tree is called the rooted phylogenetic tree. This tree is a direct type of tree that contains a special node corresponding to the most recent common ancestor of all the entities at the leaves of the tree. The use of an uncontroversial outgroup is one of the most common techniques used for rooting trees. In other words, rooted trees typically illustrate the sequence or trait data of a particular outgroup.
Another type of evolutionary tree is called the unrooted tree. Unrooted trees often illustrate the relationship between different leaf nodes. This is done without making any assumptions about the ancestry. Unlike that of the rooted trees where a sign of ancestry identify is needed, unrooted trees can always be created from rooted ones by omitting the root. Basically, an unrooted tree is generated by introducing assumptions about the relative rates of evolution on each branch or including an outgroup in the input data. An application that is often used in this process is called the molecular clock hypothesis.
Last but not least, bifurcating tree is also a type of evolutionary tree. In bifurcating tree, both rooted and unrooted phylogenetic trees can be multifurcating or bifurcating, and can be shown as labeled or unlabeled. For example, a rooted tree that has been multifurcated may have more than two children at the nodes, unlike that of the unrooted multifurcating tree where more than three neighbors can appear at the nodes.
Furthermore a rooted tree that has been bifurcated has exactly two descendants arising from each interior node that typically forms a binary tree. On the other hand, an unrooted bifurcating tree is similar to that of an unrooted binary tree. An unrooted binary tree often has a free tree with exactly three neighbors at each internal node. In terms of labeled and unlabeled trees, labeled trees has unique values assigned to its leaves, while an unlabeled tree also known as a tree shape is define as a topology only.
Overall, the number of possible trees for a given number of leaf nodes depends on the specific type of tree one is looking at. However, there are always less bifurcating trees than multifurcating trees. Similarly, there are less unlabeled than labeled trees and less unrooted than rooted trees. In terms of labeling the tree, it is always important to know that the letter "n" represents the number of leaf nodes.

## Sequence Alignment in Evolutionary Trees

Evolutionary trees can be made by the determination of sequence information of similar genes in different organisms. Sequences that are similar to each other frequently are considered to have less time to diverge. Whereas, less similar sequences have more evolutionary time to diverge. The evolutionary tree is created by aligning sequences and having each branch length proportional to the amino acid differences of the sequences. Furthermore, by assigning a constant mutation rate to a sequence and performing a sequence alignment, it is possible to calculate the approximate time when the sequence of interest diverged into monophyletic groups.
DNA can be amplified and sequences with the development of PCR methods. Mitochondrial DNA from a Neanderthal fossil was identified to contain 379 bases of sequence. When compared to the Homo sapiens, only 22 to 36 substitutions in the sequence was found as opposed to 55 differences between homo sapiens and chimpanzees over common base in the same region. Further analysis suggests that the Homo sapiens and Neanderthals shared common ancestry 600,000 years ago. This reveals that Neanderthals were not intermediate between chimpanzees and humans, but rather an evolutionary dead end, which became extinct.
Sequence alignments can be performed on a variety of sequences. For constructing an evolutionary tree for proteins, for example, the sequences are aligned and then compared via likeness to construct a tree. In the globin tree above, it is then possible to see which protein diverged first. Another example typically uses rRNA(ribosomal RNA) to compare organisms, since rRNA has a slower mutation rate, and is a better source for evolutionary tree construction.
This is best supported by Dr. Carl Woese's study that was conducted in the late 1970s. Since the ribosomes were critical to the function of how living things operate, they are not easily changed through the process of evolution. Significant changes could allow the ribosomes to not do its role, therefore having the gene sequence of it is conserved. Taking advantage of this, Dr. Woese compared the minuscule differences in the sequences of ribosomes amongst a great array of bacteria and showed how they were not all related. Looking at extreme bacteria such as methanogens, was not able to connect them to eukaryote or proselytes because they fell within their own category of archaea.

## Example of Phylogeny Tree for the Domain Eukarya

Constructing the phylogeny tree requires systematists to search for synapomorphies (shared derived characters) and symplesiomorphies (shared ancestral characters) characteristics.
Three Domain Reading the Phylogeny tree: The numbers in the diagram indicate the synapomorphies or shared derived characters unique only for those group or groups . The diagram shows that there are three domains: Bacteria, Archaea, and Eukarya. The domain Eukarya and Archaea possess (1) have introns, histones, and RNA polymerase similar to eukaryotic RNA polymerase. Furthermore, the domain Archaea possesses (2) unique lipid content in membranes and unique cell wall composition.
Domain Eukarya Four supergroups phylogeny The synapomorphies for Eukarya are (5) have a nucleus, membrane-bound organelles, sterols in their membrane, cytoskeleton, linear DNA with genomes consisting of several molecules, and a 9+2 microtubular ultrastructure flagella. Based on DNA sequence data, there are four Supergroups to this domain: Excavata, Chromalveolata, Unikonta, Archaeplastida (red algae, green algae, plants).
Supergroup Archaeplastia has (7) chloroplasts by primary endosymbiosis. Major clades: Rhodophyta (red algae), Chlorophyta (green algae), Plantae (land plants). Archaeplastida phylogeny
Supergroup Excavata: Excavata There are three phyla for this Supergroup: Parabasalia, Euglenophyta, and Kinetoplastida. Euglenophyta doesn’t have cell wall, but have (8)flexible pellicle within the cell membrane. It has chlorophyll A amd B as in plants - which it obtained by secondary endosymbiosis, green lineage. Parabasalia possesses (9) a reduced or lost mitochondria. Kinetoplastida has (10) single large mitochondrio/kinetoplast, which edit mRNAs.
Supergroup Chromalveolata: Chromalveolata phylogeny There are three clades: alveolata, straminopila, and rhizaria.
Rhizaria's Phylum Foraminifera possesses (11) multichambered shells made of organic material and CaCO3.
Synapomorphies for straminopila and rhizaria are (12) chloroplasts by secondary endosymbiosis, red lineage.
Stramenopila has (13) two unequal flagella, one longer tinseled. There are three major phyla for Stramenopila. Phylum Bacillariophyta (diatom) has (14) cell walls of hydrated silica in organic matrix, made up of two halves: “box and lid.” Phylum Phaeophyta (Brown algae)has (16) multicellular sea weeds. Phylum Oomycetes (water molds, downy mldews) has (15) a loss of chloroplasts.
Alveolata has (17) a membrane-bound sac under plasma membrane. There are three phyla. Phylum Dinoflagelleta possesses (19) plates of cellulose-like material, grooved. Phylum Ciliophora has (20) two types of functionally different nuclei: macronucleus (controls metabolism) and micronucleus (function in sexual reproduction). Phylum Apicomplexa has (18) apical structure for penetrating host cells.
Supergroup Unikonta has (6) a triple pyrimidine biosynthesis fusion gene and has one flagellum
Unikonta phylogeny Three major clades: Amoebozoans, Fungi, Animals.
Amoebozoa has (21) broad pseudopodia. It's Phylum Gymnamoeba (22) feed and move by lobed pseudopodia.
Opisthokonta (Fungi and Animalia) possess (23) flagellum posterior. Fungi has (24) cell walls made of chitin, absorptive heterotrophy, and are multicellular. There are four Phyla of Fungi. Asides from Phylum Chytridiomyota (water molds), all other Fungi Phyla has a (25) loss of flagellum and time separation between plasmogamy and karyogamy. Phylum Zygomycota has (26) heterokaryotic state of reproduction limited to zygosporangium. Both Basidiomycota and Ascomycota possess (27) conidia, extensive (n+n) state, size and duration, septate hyphae, and macroscopic fruiting bodies. Phylum Basidiomycota has (28) long-lived dikaryotic mycelium in dikaryotic state, meiospores produced in special cell called basidium, and are sex predominant (asexual spores rare). Phylum Ascomycota has (29) meiospores produced in special cell called ascus.
Kingdom Animalia are (30) multicellular, possess extracellular matric with collagen, proteoglycans, and special types of junctions between cells (cell adhension proteins).
Animalia phylogeny
Phylum Porifera (sponges) has (31) spicules, internal aquiferous system. Subkingdom Eumetazoa has (32) body symmetry, primary germ layer (true endoderm and ectoderm), true tissues and organs, epithelial tissue, and nervous tissue. Radiata has (33) primary radial symmetry. Phylum Cnidaria has (34) a mesoglea, and a cnidocytes (with nematocysts). Bilateria has (35) bilateral symmetry, body cavity (coelom), mesoderm (triploblastic), and muscle. Two mahor phylogenetic branches are Protostomia and Deuterostomia. Protostomia has (36)a schizocoelous, and the blastopore becomes its mouth. Deuterostomia has (37) entercoelous, indeterminate cell fate, radial cleavage, and the blastopore becomes the anus. Phylum Echinodermata has (38) a water vascular system, tube feet, and has radial symmetry in adults (bilateral larvae). Hemichordata has (39) pharyngeal slits at some state of life. Phylum Chordata has (40) muscular post-anal tail, dorsal follow nerve cord, and notochord.
Phylogeny tree for Protostomia. Protostomia phylogeny
Phylogeny tree for Chordata. Chordata phylogeny

## References

Waggoner. Ben. "Archaea: Systematics." 15 Nov. 2009. <http://www.ucmp.berkeley.edu/archaea/archaeasy.html> http://en.wikipedia.org/wiki/Phylogenetic_tree