Applications of Phylogenetics

Classification and Systematics

Purpose: To identify monophyletic taxa (clades).
- Monophyletic group: Includes an ancestor and all its descendants.
Examples:
- Snakes: Form a monophyletic group.
- Lizards: Not phylogenetically accurate, as they form a paraphyletic group.
  - Paraphyletic group: Includes a common ancestor but not all descendants.
  - The term "lizard" excludes snakes, even though the common ancestor of iguanas also gave rise to snakes.
- Reptiles: Also a paraphyletic group because the common ancestor of crocodiles also gave rise to birds.
- Better classification:
  - Squamata: Snakes and lizards (monophyletic).
  - Archosaurs: Crocodiles and birds (monophyletic).
Resolving Misinterpretations:
- Phylogenies help resolve evolutionary history that may be misinterpreted due to convergent evolution.
- Example: Falcons and eagles were once grouped together due to ecological and morphological similarities (falconiforms).
  - Phylogenetics revealed falcons are close to songbirds, while eagles are distant relatives.
Understanding Genealogical Relationships:
- Understanding genealogical relationships allows expectations of ecological and genetic similarities among phylogenetically related taxa.
- Example:
  - Coleoptera (beetles): Diverse morphologies and colors, but all belong to one monophyletic group, implying ecological similarities.
  - Horseradish and Arabidopsis (model plant): Belong to the same family (Brassicaceae), indicating similar genomes.

Dating Evolutionary Events

Molecular Clock Hypothesis:
- DNA sequences evolve at a relatively constant rate over time.
- Linear relationship between time and nucleotide differences (mutations).
- $x$ -axis: Time (millions of years ago).
- $y$ -axis: Nucleotide differences (mutations).
- Example: Mammals show a linear relationship between time and nucleotide differences.
- Estimating Divergence Time: If there is a 45 base pair difference, the divergence time is estimated to be around 74 million years ago.
Strict Molecular Clock Assumption:
- Assumes all lineages evolve at the same rate.
- However, evolutionary rates vary among species, lineages, and traits.
- Rates are driven by mutation rate and generation time, which differ across species.
- Example: Apes evolve much slower than other mammals and primates.
Relaxed Molecular Clock:
- Allows different lineages to have different evolutionary rates.
Converting Genetic Differences into Time:
- Assumes a rate of evolution (strict or relaxed clock).
Using Fossils:
- Fossil ages can anchor nodes in the phylogenetic tree.
- The age of other nodes can be estimated relative to known fossil ages.
- With enough sequence data, mutation rates, and known fossil ages, divergence times can be confidently estimated.

Discovering the History of Genes and Cultures

Gene Trees:
- Gene trees differ from species trees.
  - Gene trees look at a single gene.
  - Species trees look at the whole genome or concatenated genes.
- Gene trees help identify whether adaptation resulted from new mutations or standing genetic variation.
Example: EDA Locus in Sticklebacks:
- Two morphs: low plated (freshwater) and high plated (marine and freshwater).
- Low plated morph caused by an allele of the EDA gene, important for ectodermal differentiation.
- Phylogenetic Tree:
  - Low plated sticklebacks form a monophyletic group.
  - High plated sticklebacks form a monophyletic group.
  - Suggests low plated morph has a single origin.
- Evolution from Standing Genetic Variation:
  - Copies of the low plated allele were present in the ancestral marine population.
  - Became better adapted to freshwater environments.
History of Cultures:
- Linguistic traits: Languages are inheritable and variable, used as characters to create phylogenetic trees.
- Example: English diverged from Western Germanic languages, which diverged from Proto-Germanic, and evolved from Proto-Indo-European languages.
- Austronesian Languages: Originated in Taiwan more than 5,000 years ago and spread into Southeast Asia, India, and the Pacific Ocean.
- Mapping Linguistic Traits:
  - Map linguistic traits to complexity of political systems (no chief, simple chiefdom, complex chiefdom, state).
  - Mixed pattern: More complex political systems often develop from simpler ones, with occasional reversion to simpler forms.

Reconstructing Ancestors

Using Contemporary Sequences:
- Patterns of relationships between contemporary amino acid or DNA sequences.
- Estimate how the ancestor would have looked using statistical estimation methods (ancestral state reconstruction).
Applications:
- HIV Vaccine Development:
  - HIV has diverse viral strains.
  - Identify how the ancestor would have looked to create vaccine genetically close to a broad range of strains.
  - Ancestral protein helps focus on a broad range rather than one specific strain, since HIV mutates quickly.
- Developing New Enzymes:
  - Need enzymes with higher temperature or thermal stability.
  - Estimate how extinct enzymes would have looked like.
Geographic Distribution as a Character:
- Overlay genetic information with geographic distribution for tracing pandemic outbreaks.
- Example: Ebola Pandemic in 2014 in Africa:
  - Traced back to an outbreak in 1975 in Congo.
  - Over 37 years, 24 smaller outbreaks occurred in different places within Africa.
- Nextstrain: Open-source platform to track and visualize the evolution of pathogens, with geographic distribution data overlaid on phylogenetic trees.
  - Showed that during the COVID lockdown period (2020-2021), fewer new Ebola strains and outbreaks occurred.

Studying Adaptations

Comparative Method / Phylogenetic Comparative Methods:
- Compare different species to test hypotheses about adaptation.
- Understand whether traits are correlated due to adaptation or common ancestry.
Example: Birds Fly and Lay Eggs, Mammals Do Not Fly and Give Live Birth:
- No adaptive link between flight and egg laying.
- Correlation is likely because the ancestor of all birds flew and laid eggs.
Controlling for Phylogeny:
- Species are not independent data points due to shared common ancestry.
- Phylogenetic comparative methods: Statistical methods that combine phylogenetic trees with trait values.
Example: Sex Determination and Sex Ratio in Tetrapods:
- Phylogenetic tree of tetrapods with sex determination system (ZW or XY) and sex ratio bias.
- Birds (ZW) are male-biased, while mammals (XY) are female-biased.
- Lizards and amphibians show mixed patterns.
- General trend: XY species tend to have female-biased sex ratios, and ZW species have male-biased sex ratios, suggesting an adaptive correlation.

Studying Trends

Rates of Evolutionary Change:
- Vary between lineages, within lineages, and between traits.
- Conservative traits evolve slowly (e.g., five-toed limbs in tetrapods, seven neck vertebrae in mammals).
- Traits can evolve quickly (e.g., body size in mammals).
Mosaic Evolution:
- Different characters evolve at different rates in one lineage.
- Evolution is goal-less; it creates species more adapted to their environment.
Traits and Phylogenies:
- Understanding how intermediate stages of traits look like by studying phylogenetic trees.
- Example: Gradual changes in bill length in sandpipers.
Homoplasy:
- Independent evolution of similar traits; the common ancestor didn't have the trait.
- Convergent evolution.
- Example: Eyes in cephalopods and vertebrates.
  - Similarities: Iris, lens.
  - Differences: Vertebrates have an optic nerve, cephalopods do not.
Gain and Loss of Traits:
- Dollo's law of irreversibility: Once a trait is lost, it's unlikely to be regained (not always true).
- Traits can be lost and regained due to re-evolution, convergence, or parallelism.
- Examples of regain after loss:
  - Limbless lizard ancestor, descendant regains limbs.
  - Viviparous ancestor, descendant regains oviparity.
  - Ancestor loses pigments, descendant regains pigmentation.