Classification and Cladistics

Define classification and explain its importance: 

• Classification is categorizing organisms based on taxons due to the vast amount of biodiversity on Earth (grouping them together for organization + differentiate between species)

• Help of modern technology → more accurate 

• Importance:

  • Species evolution

  • Accurate number of species (No repeated groups/species because it is not based on observable traits)

  • Conserve species due to similar genetics/ancestor

  • Medical research more quick because easier to identify through close relatives 

  • Identify and treat diseases more quickly

Explain the difficulties of classifying species into taxa (Domain/Kingdom/Phylum/Class/Order/Family/Genus/Species):

• Morphology

  • Physical characteristics = subjective= more errors (similar morphology ≠ share common ancestor) 

  • Genome sequencing used to solve this problem (use genes rather than observable traits/phenome)  

• Taxonomic Rank 

  • Complicated if group of organisms must be moved from taxa/share features in different taxa (risk of re-arranging groups in existing taxon into different rank for new groups) 

  • Fertile hybrids are difficult to place in taxa classification because they are new species with characteristics of 2+ taxa 

• Species 

  • Deviation of species is highly subjective 

  • Introgression: When species produces fertile offspring with another offspring for multiple generations. Not entirely another species either. 

Discuss how cladograms can be used in classification of organisms: 

• Clades in cladograms: groups of species that share common ancestor is found using DNA sequencing technology 

• Includes both living + extinct species

• Classifying organisms using clades = more closely related to each other + clades can be moved/re-organized into different groups or clades can split/merge. 

• Uses sequence DNA from DNA/RNA/mRNA. More similar sequence = more similar species. Some closely related species have similar morphology (physical characteristics) but not often the case due to mutation/phenotype also very subjective 

• Clades must be from primitive traits(trait shared since common ancestor) and derived traits (different traits after divergence from common ancestor) 

• Clades avoids mistakes such as descendents of common ancestor in different clades/organisms from difference ancestor in same clade

Explain the importance of molecular clock:

• Constant rate of mutation of species= molecular clock 

• Number of mutation = indication of amount of time passed between 2 species that diverged 

• Bigger difference in sequence = bigger time difference since species diverged 

• DNA hybridization used to find difference between sequence ans see  how long ago they diverged:

  • Sections of single-stranded DNA taken from corresponding gene of 2 diff species

  • Both DNA are hybridized to form double-stranded complementary DNA. 

  • The points where they don’t bind = difference in DNA sequence. Number of differences recorded 

List the features of cladograms:

• Root: base of cladogram. Common ancestor of all organism in cladogram 

• Nodes: common ancestor. Closer the clades = closely related than other clades. 

• Terminal branches: Most recent species in evolutionary lineage 

• Ingroups: Groups whose relation that is being investigated

• Outgroups: Group that is closely related to group of interest (ingroup) but branched off earlier in evolutionary history. Ref point by comparing and contrasting differences/similarities of in and out groups (which are unique to species aka derived traits or shared traits aka primitive traits)

Explain reclassification using the example of figwort family:

• Reclassification: Using DNA sequencing to classify organisms that were incorrectly placed (only relied on observed traits) into not true clades. Reclassified into diff groups, or groups are split/merged. It is important to be classified in correct clade so group = closely evolutionary relatives

• Figwort family:

  • One of the biggest family in angiosperm phylum classified based on observable traits (tube-shaped flower structure). Ex: foxgloves/yellow rattle 

  • 3 chloroplast genes were analyzed to show that original figwort family ≠ true clade, instead it was paraphyletic (all groups did not contain descendents of common ancestor). Must be placed in diff branches. New families created/genus moved to other families. 

  • New figwort family = half its size as before 

Detail the classifications of archaea/eubacteria/eukaryotes:

Archaea  (prokaryotes) 

• Circular chromosome 

• Glycerol-ether lipids cell membrane

• 70S with small subunit (similar to eukaryote ribosome) ribosome 

• Always have cell walls without peptidoglycan

• Has histones

• Sometimes have introns 

Eubacteria (prokaryotes) 

• Circular chromosomes

• Glycerol-ether lipids cell membrane

• 70S ribosome

• Always have cell walls without peptidoglycan

• No histones

• Rarely have introns 

Eukaryotes (fungi/animals/plants) 

• Linear chromosomes (circular for mitochondria/chloroplast) 

• Glycerol-ether lipids cell membrane

• 80S ribosome in cytoplasm (70S in mitochondria and chloroplast) 

• Sometimes have cell walls without peptidoglycan

• Has histones

• Has introns