Systematics and Phylogeny

Systematics

• Systematics is the science of organizing and classifying organisms based on their evolutionary relationships
• Systematics relies on:
  • Fossils
  • DNA
  • Anatomy and morphology
  • Behavior

Phylogeny

• Phylogeny is the evolutionary history and relationship of an organism or group of organisms
• Phylogenetic relationships provide insight into shared ancestry
• They do not necessarily indicate how similar or different organisms are
• A phylogenetic tree visually represents these relationships

Phylogenetic Tree

• Diagrams that reflect the evolutionary relationships among organisms or groups
• They are hypotheses about the evolutionary past
• They illustrate when different organisms evolved and their relationships to each other
• Phylogenetic trees can be rooted or unrooted

Parts of a Phylogenetic Tree

• A branch point signifies where two lineages diverged
• A basal taxon is a lineage that evolved early and remains unbranched
• Sister taxa are two lineages stemming from the same branch point
• A polytomy is a branch with more than two lineages

Cladistics

• Cladistics sorts organisms into clades
• Clades are groups of organisms descended from a single ancestor
• Clades must include all descendants from a branch point
• Clade size varies depending on the reference branch point

Descent with Modification

• A change in an organism's genetic makeup leads to a new trait that becomes prevalent in the group
• Many organisms inherit this trait from that point forward
• New variations keep emerging; those that are adaptive persist and can lead to new traits
• The development of new traits determines a new branch point

Shared Characteristics

• Shared ancestral characteristics are traits all organisms in a taxon or clade possess
• Shared derived characteristics are traits derived at a certain point
• Shared derived characteristics- do not encompass all ancestors in the tree

Maximum Parsimony

• Evolution favors pathways with the fewest major events that align with available evidence
• Scientists identify the most straightforward sequence of evolutionary events that led to the occurrence of homologous traits in a group of organisms

Limitations of Phylogenetic Trees

• Groups can appear more different than other groups that are not as closely related
• Branches do not represent time spans, only the sequence of evolutionary events
• Phylogenetic trees only represent a part of the larger interconnected web of life

Limitations to the Classic Model

• Species evolve clonally
• Horizontal gene transfer (HGT) is the transfer of genes between unrelated species
• Genome fusion theories exist between symbiotic or endosymbiotic organisms

Horizontal Gene Transfer (HGT)

• HGT is when genetic material transfers from one species to another without vertical transmission
• HGT enables even distantly related species to exchange genes
• HGT is a key source of genetic variation, especially in prokaryotes and is the raw material for natural selection

Prokaryotic HGT Mechanisms

• Transformation: DNA uptake
• Transduction: Bacteriophage (virus)
• Conjugation: Pilus
• Gene Transfer Agents: Phage-like particles

Eukaryotic HGT Mechanisms

• From food organisms: unknown
• Jumping genes: Transposons
• Epiphytes/parasites: Unknown
• From viral infections

HGT in Prokaryotes

• HGT mechanisms are common in Bacteria and Archaea
• The Endosymbiont Theory suggests eukaryotes descended from multiple prokaryotes

Transformation

• Bacteria takes up naked DNA

Transduction

• Virus transfers the genes

Conjugation

• Hollow tube, or pilus transfers genes between organisms

Gene Transfer Agents (GTAs)

• GTAs are small, virus-like particles that transfer random genomic segments from one prokaryote species to another
• GTAs are linked to genetic changes, sometimes at a very high frequency
• The first GTA was found in 1974 in purple, non-sulfur bacteria
• GTAs which are thought to be bacteriophages that lost the ability to reproduce on their own
• They carry random pieces of DNA from one organism to another
• GTAs ability to act with high frequency is demonstrated in marine bacteria

HGT in Eukaryotes

• HGT is rarer and more challenging in eukaryotes than in prokaryotes
• HGT has a smaller evolutionary impact than in prokaryotes

Jumping Genes

• Transposons or "jumping genes" have shown a transfer between rice and millet plant species

Epiphytes/Parasites

• Fungal species consume yew trees
• Fungi acquire the ability to make Taxol from the bark

From Food Organisms

• Aphids acquire the ability to make carotenoids, consuming fungi as food

Aphids

• Red aphids produce red carotenoid pigment through desaturase
• Genes for this pigment are present in certain fungi
• Aphids reverted back to green if genes for making carotenoids are inactivated by mutation
• Red aphids are more noticeable to predators; however, are more resistant to insecticides

Genome Fusion and Evolution of Eukaryotes

• Fusion takes place between different prokaryote species, two symbiotic organisms become endosymbiotic

Endosymbiont Theory

• Mitochondrial DNA
• Ancestral bacteria and Archaebacteria form eukaryotic cells
• Archaea and Gram-positive bacteria form gram-negative bacteria

Eukaryotes

• James Lake proposed using DNA analysis and conditioned reconstruction (CR)
• Eukaryotic cells developed from an endosymbiotic gene fusion between Archaea and Bacteria

Web of Life

• W. Ford Doolittle proposed a phylogenetic model that resembles a web instead of a tree
• Eukaryotes evolved from many species sharing genes through HGT

Ring of Life

• Lake proposed a ring-like model where all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes