# Chapter 26

## Overview

- Taxonomy and Systematics
- Phylogenetic Trees
- Horizontal Gene Transfer

### Taxonomy

The Science of describing, naming, and classifying living an extinct organisms and viruses.

#### Systematics

Study of biological diversity and the evolutionary relationships among organisms, both extinct and modern.

- Taxonomic groups are based on hypothesis regarding evolutionary relationships from systematics
- Hierarchical system involving successive levels
- Each group at any level is called a **taxon**
- Highest level is **Domain**
    - All life belongs to 3 domains
    - Bacteria, Archaea, and Eukarya 
        - The Eukarya Domain is often divided into Kingdoms in the next level  
            This is typically called the 4 Kingdom concept

[![Screenshot-from-2019-01-29-11-51-38.png](https://bookstack.aronwk.com/uploads/images/gallery/2019-01-Jan/scaled-840-0/WkMUYtKa68gITVpG-Screenshot-from-2019-01-29-11-51-38.png)](https://bookstack.aronwk.com/uploads/images/gallery/2019-01-Jan/WkMUYtKa68gITVpG-Screenshot-from-2019-01-29-11-51-38.png)

## Four Kingdoms

- Domains Bacteria and Archaea 
    - Prokaryotic cells 
        - Lack nucleus
- Kingdom Protista, Fungi, Plantae, Animilia 
    - Eukaryotic cells 
        - True nucleus

### Types of cells

#### Prokaryotic 

- Lack Nucleus
- Lacks membrane-bound organelles
- Typically singled celled

#### Eukaryotic 

- Well defined nucleus
- Membrane-bound organelles
- internal membrane system (compartments)

## Binomial Nomenclature

- Genus name + Specific epithet 
    - ex. *Homo sapiens* ('wise humans')
- Genus name is always capitalized
- Specific epithet is never capitalized
- Both names are either *italicized* or <span style="text-decoration: underline;">underlined</span>

## Phylogenetic Trees

- Phylogeny 
    - Evolutionary history of a species or group of species
- To propose a phylogeny, biologist must use the tools of **systematics**
- Trees are usually based in morphological and genetic data 
    - Subjective vs. Objective data
- Diagram that describes the phylogeny
- A hypothesis of evolutionary relationships among various species
- Based on available information

#### Monophyletic Group or Clade

- Group of species (taxon) consisting of the most recent ancestor and all of its descendants
- Smaller and more recent clades are nested within larger clades that have a common ancestor

#### Paraphyletic group

- Contains a common ancestor and some, but not all of its descendants

[![Screenshot-from-2019-01-29-11-52-15.png](https://bookstack.aronwk.com/uploads/images/gallery/2019-01-Jan/scaled-840-0/m2Obq2j58FU3mZ4U-Screenshot-from-2019-01-29-11-52-15.png)](https://bookstack.aronwk.com/uploads/images/gallery/2019-01-Jan/m2Obq2j58FU3mZ4U-Screenshot-from-2019-01-29-11-52-15.png)

- Over time, taxonomic groups will be reorganized so that only monophyletic are recognized
- Reptiles were a paraphyletic group because birds were excluded
- **In the class and lab, we are going to separate birds and reptiles**

[![Screenshot-from-2019-01-29-11-53-44.png](https://bookstack.aronwk.com/uploads/images/gallery/2019-01-Jan/scaled-840-0/8Wv6XVyvrUgZQDcl-Screenshot-from-2019-01-29-11-53-44.png)](https://bookstack.aronwk.com/uploads/images/gallery/2019-01-Jan/8Wv6XVyvrUgZQDcl-Screenshot-from-2019-01-29-11-53-44.png)

## Systematics

### Morphological Analysis

- First systematic studies focused on morphological features of extinct and modern species
- Most of early classifications were based upon morphological features

### Molecular Analysis

- Analysis of genetic data (DNA, Amino Acids, rRNA) to identify and study genetic similarities and propose phylogentic trees
- DNA and Amino Acid sequences from closely related species are more similar to each other than sequences from more distantly related species

### Horizontal Gene Transfer

- any process in which an organism incorporates genetic material from another organism without being the offspring of that organism (by means of asexual reproduction)

### Vertical Evolution

- Changes in groups due to descent form a common ancestor (sexual reproduction)