# Classification & Phylogeny ## Historical vs. Modern Classification - In the past, scientists classified organisms based on **shared visible features** - This approach focused on observable anatomical characteristics - While useful, it often failed to reflect true evolutionary relationships - Modern classification aims to classify organisms based on **phylogeny**

Phylogeny is the evolutionary history and relationships between organisms

## Principles of Phylogenetic Classification - Phylogenetic classification groups organisms according to their evolutionary history - Species sharing a **more recent common ancestor** are classified together - Species with a **more distant common ancestor** are placed in separate groups - This approach often requires changes to historical classification systems - E.g. birds and bats were once grouped together based on flight ability - However, birds and bats are not close evolutionary relatives - Phylogenetic evidence shows they evolved flight independently ## Molecular Evidence in Classification ### Advances in Technology - Developments in **DNA, RNA, and protein sequencing** technology have revolutionised classification - Scientists can now classify organisms according to phylogeny more accurately than using visible characteristics alone - This molecular approach provides objective, quantifiable data about evolutionary relationships - Molecular analysis enables construction of **phylogenetic tree diagrams** - These visual representations show evolutionary relationships between species - Branch points indicate common ancestors - Branch lengths can represent time or genetic distance ### Types of Sequence Data Three types of molecular sequence data are used to investigate evolutionary relationships: | Sequence Type | Description | |---------------|-------------| | **DNA** | Base sequences in genomic DNA | | **mRNA** | Base sequences in messenger RNA transcripts | | **Amino acids** | Amino acid sequences in proteins | - Sequencing technology determines the order of: - DNA bases (A, T, C, G) - mRNA bases (A, U, C, G) - Amino acids within proteins

Comparing multiple proteins or genome regions provides more accurate estimates of evolutionary relatedness than single comparisons

### Selecting Appropriate Molecules for Comparison - Scientists choose **specific proteins or genome sections** for comparison between organisms - Key criteria for selecting molecules: - Must be present in a **wide range of organisms** - Must show **sufficient variation between species** to be informative - Should be functionally important (so conserved enough to compare) - **Cytochrome c** is frequently used for evolutionary comparisons - Integral protein in the electron transport chain during respiration - Used by all eukaryotic organisms - Shows variation between species while remaining functionally similar ### Interpreting Sequence Similarities

The more similar the sequences between two organisms, the more closely related they are

- High sequence similarity indicates: - Species separated into distinct lineages **more recently** - Less time for mutations to accumulate - Closer evolutionary relationship - Low sequence similarity indicates: - Species separated into distinct lineages **longer ago** - More time for mutations to accumulate and change sequences - More distant evolutionary relationship - Sequence analysis and comparison generates **phylogenetic trees** showing evolutionary relationships ## DNA Analysis and Comparison ### Extraction and Analysis Process - **DNA is extracted** from cell nuclei taken from an organism - Can be extracted from blood or skin samples from living organisms - Can also be extracted from fossils for ancient DNA analysis - The extracted DNA is **processed and analysed** to obtain the base sequence - Base sequences are **compared** between organisms to determine evolutionary relationships ### Practical Applications - DNA sequence comparison has revealed surprising evolutionary relationships - Example: Human and chimpanzee genome comparison (2005) - Humans and chimpanzees share approximately **99% of their DNA sequences** - This makes chimpanzees our closest living relatives - The 1% difference accounts for all the observable differences between the species - Example: Human and bonobo genome comparison (2012) - Humans and bonobos share **98% of their genome** - Slight differences exist compared to the differences with chimpanzees - Both species are extremely close relatives to humans ### DNA vs. Protein Sequencing | Aspect | DNA Sequencing | Protein Sequencing | |--------|----------------|-------------------| | **Traditional ease** | More difficult historically | Easier to isolate proteins from cells | | **Modern preference** | Now preferred method | Less commonly used | | **Information content** | Can reveal differences in introns | Only shows coding sequences | | **Genetic code** | Shows all genetic variation | May hide variation due to degenerate code |

Amino acid sequences may be identical between species even when DNA sequences differ due to introns and degenerate codons

- **Why DNA sequencing has advantages:** - Genes for the same protein may have slightly different base sequences in different species - Differences in **introns** (non-coding regions) are not translated into protein differences - The **degenerate genetic code** means multiple codons can code for the same amino acid - DNA sequencing captures all this variation that protein sequencing might miss ## Phylogenetic Classification in Practice ### Replacing Historical Groupings - Phylogenetic classification means historical organism groups often need revision - Groups based on superficial similarities may not reflect evolutionary history - Molecular evidence can overturn long-standing classifications ### Special Considerations - This technology is especially useful for: - Comparison with **extinct species** using ancient DNA - Distinguishing between species that are **very physically similar** but genetically distinct - Resolving classification disputes where visible features are ambiguous ### Building Phylogenetic Trees - Scientists use sequence data to construct phylogenetic trees step by step: 1. Collect sequence data from multiple species 2. Identify similarities and differences 3. Calculate genetic distances between species 4. Determine branching patterns based on shared characteristics 5. Construct a tree showing the most likely evolutionary relationships - The resulting trees show: - **Branch points**: represent common ancestors - **Branch lengths**: can represent evolutionary time or genetic distance - **Terminal nodes**: represent current or recent species - **Overall structure**: illustrates the pattern of evolutionary divergence