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Phylogenetics Notes

Introduction

Phylogeny is the evolutionary history of life. It can be thought of as a tree that shows the evolutionary relationships of organisms.

Taxonomy refers to naming and classifying organisms.

Systematics is classification based on evolutionary relationships (phylogeny). Systematists attempt to discover phylogenetic relationships.

Traditionally, individuals of the same kind are categorized as a species. In sexually-reproducing organisms, two individuals of the same species are capable of interbreeding. Closely-related species are grouped into a genus. Closely-related genera are grouped into a family, then order, class, phylum (or division in plants), kingdom, and finally domain.

Many taxonomists categorize organisms into 3 domains: Bacteria, Archaea, and Eukarya. The Bacteria and Archaea are prokaryotes. The domain Eukarya includes Protists, Fungi, Plants, and Animals.

Molecular systematics- uses data from molecules such as DNA and protein to determine evolutionary relationships.

Cladistics, or Phylogenetic Systematics is a technique of grouping species by similarities. Organisms that have many similarities are assumed to be more closely related than those that have fewer similarities. A group is called a clade.

Caution must be used when using morphological characteristics because phenotypic similarity might not be due to genetic relationships. For example, snakes appear to be more similar to apodans (legless amphibians) than to reptiles but they are more closely related to reptiles.

Members of a clade have shared derived characteristics. These are characteristics that occur in members of the clade but not in their ancestors. Because the ancestor does not have the characteristic, it must have evolved after the clade evolved. Any individuals that possess the characteristic must belong to the clade.

Phylogenetic  Tree

Phylogenetic trees show evolutionary relationships among different kinds of organisms. The branch points on the tree indicate the point where two new species diverge. The tree below shows that species A evolved into species B and species C. Species B evolved into species D and species E.

The length of a line might not indicate time. For example, the length of the line from A to B might 300 million years and the length of the line from B to E might be 10 million years.

Phylogenetic trees may contain errors. As new evidence is discovered, it is often necessary to change trees and reclassify organisms.

Sister taxa contain an immediate common ancestor.

The earliest taxon to evolve in a phylogenetic tree is called a basal taxon.

A monophyletic is a group that includes an ancestral species and all of its descendents (see figure 26.10). A polyphyletic group is a group that includes species that do not all share a common ancestor within the group.

Structures and Characteristics

Ancestral characteristics- a characteristic that is present in the ancestors of a group.

Shared derived characteristics are present in the members of a group but not in the ancestors of the group. Shared derived characteristics are used to determine evolutionary relationships.

Homologous Characteristics

Generally, similar morphology indicates close evolutionary relationships but not always. For example, bats are more closely related to mice than they are to birds even though bats and birds both have wings.

Homologous structures- structures descended from the same ancestral structures. Example- the limbs of vertebrates

Analogous structures are due to evolutionary convergence. They do not indicate evolutionary relationships. Examples:

The eyes of mammals and the eyes of some mollusks (cephalopods) are analogous structures because they did not evolve from the same ancestral structure.

The wings of birds and the wings of insects are analogous structures because they did not  evolve from the same ancestral structure.

Many placental mammals have a body form that is similar to marsupials. The similarity is due to the similar environment in which they live. It is not due to evolutionary relationship. Examples: Tasmanian wolf and wolf, moles and marsupial moles, flying squirrel (placental) and flying phalanger (marsupial).

Complex structural similarity indicates homology. Example- The bones in the skull of a chimpanzee and a human are nearly identical. This amount of similarity can only be due to inheritance from a common ancestry.

Similarly, genes that are very similar are probably homologous. Computer programs can be used to determine the similarity of DNA from different sources. Example- see figure 26.8.

Creating Phylogenetic Trees

Shared derived characteristics are used to create phylogenetic trees.

Phylogenetic trees are typically created with an outgroup. The other groups are ingroups. Figure 26.11 shows a tree created for vertebrates. Lancelets are an outgroup, the other groups (vertebrates) are ingroups. A tree with an outgroup is rooted. One advantage of a rooted tree is that all of the evolutionary relationships within the group in question are shown.

Branch Lengths

Branch lengths can be proportional to the amount of change in the DNA. See figure 26.12.

Branch lengths can reflect time. See figure 26.13.

Arranging Branches on a Phylogenetic Tree

There will be many different ways to arrange the branches when creating a tree. Different methods have been developed for creating trees.

Maximum parsimony (= Occam’s razor)- the simplest- The branches are arranged in a way that requires the fewest evolutionary events to explain current characteristics.

Maximum likelihood- construction is based on what is most likely due to underlying assumptions. Figure 26.14 shows two trees that have equal parsimony but one is more likely if you assume that the rate of genetic change is constant.

Molecular Systematics

Molecular systematics involves classification of species based on the similarity of molecules such as DNA or proteins.

It is useful for species that do not have many common physical characteristics such as plants, fungi, animals. It is also useful for current species that do not have a good fossil record.

Different genes evolve at different rates. For example, the rRNA gene changes slowly. Therefore it is useful for looking at relationships from early in the evolution of a group (earlier geologic time). Mitochondrial DNA evolves rapidly so it is more useful for exploring recent evolutionary changes.

Molecular Clocks

Some regions of DNA change at a fairly constant rate. The amount of change in these segments can be used as a clock to determine when two groups diverged from a common ancestor. The length of time since divergence is correlated with the number of nucleotide substitutions in the DNA.

The clock must be calibrated because some genes evolve much faster than other genes. The clock can be calibrated using known dates of divergence from the fossil record. Example: see fig. 26.19.

If the exact amino acid sequence of a protein is essential to survival, the gene will probably evolve slowly because most mutations will be harmful and eliminated by natural selection. Neutral mutations will accumulate over time but there will be relatively few neutral mutations because the amino acid sequence must be exact.

If a variety of amino acid sequences can produce a functioning protein, the gene will probably evolve rapidly because more of the mutations are likely to be neutral.