Week 13: Phylogenetics and the History of Life

When does evidence suggest life first evolved?

3.5 billion years ago

What characteristics so all organisms share?

Composed of one or more cells, carry out metabolism, transfer energy with ATP, and encodes hereditary information in DNA.

How do biologist group organisms?

Based on shared characteristics

Systematics

reconstruction and study of evolutionary relationships

Phylogeny

Hypothesis about relationships among taxonomic groups. Depicted as a phylogenetic tree or cladogram

Rooted Phylogenetic Tree

Single lineage (at the base) represents common ancestor, branching indicates evolutionary relationships

Branch point

Where split occurs and lineage evolves into new one

Unrooted Phylogenetic Tree

Show relationships but not a common ancestor

Taxon (phylogenetic tree)

Group(s) of organisms (species, family, domain, etc.)

Clade (phylogenetic tree)

Any branch or lineage (lines in cladogram)

Branch point (node) - phylogenetic tree

Splitting represents single lineage evolving into two clades

Cladogram

Show relationships between organisms based on shared traits. Do not reflect the amount of difference between groups or describe the process of evolution

Phylogenetic Trees

Show relationships between organisms over evolutionary time, reflecting the amount of difference/change. The branch lengths matter (longer = more change)

Single cut rule

If you can make a single cut to isolate the group, it is a clade

Limitations of phylogenetic trees

Often closely related taxa look similar, but not always. If evolved under different circumstances (selection pressures), the taxa may look different. Unless specified, the length of the branch does not indicate amount of time passed since the split.

Taxonomy

Science of classifying organisms into taxa

Linnaean system

Uses a nested hierarchical system where in each sublevel, organisms become more similar.

Dear King Philip Cried Out, “For Goodness Sake!”

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (then subspecies).

Binomial nomenclature of species

Species name = genus + species ‘epithet’

genus is capitalized and italicized

Determining Evolutionary relationships

Systematists use diversity of evidence to determine relationships among organisms and higher taxa

Morphologic (form and function)

Physiologic, behavioral, and genetic characters

Some organisms may be closely related, despite minor genetic change causes morphological difference

Homologous Characters

Similar due to evolutionary origin (same ancestral source), based on genetics and developmental origin, more complex the character means it is more likely of the same origin, and often look similar but not always.

Analogous characters

Similar due to functional or ecological constraints/pressures, characters can be very similar in appearance due to evolutionary convergence which occurs in unrelated (or distantly related) taxa when characters are shaped by similar ecological or evolutionary constraints (selection pressures)

Convergent Evolution

Structures that evolve from the same evolutionary pressure but not from a common ancestral trait

ex. wings in birds and wings in insects

Evolutionary reversal

Ancestral traits are sometimes lost in descendants in one group

ex. loss of limbs in snakes (all other reptiles have legs)

Molecular comparisons

Using nucleotide sequences (DNA RNA) as characters provides new insight to evolutionary relationships

Why do phylogenetics matter?

Understanding of true evolutionary relationships is important

Cladistics

Process to arrange taxa by homologous characters into clades (branches) → cladogram. Goal is to produce cladograms where all clades are monophyletic, a group of organisms that evolved from single common ancestor.

Monophyletic Group (Monophyly)

Includes all descendants of a given ancestor, includes the most recent common ancestor and all descendants, each clade represents a single “cut”

Descent with Modification

Organism (taxa) evolve from common ancestors, then diversify…repeated many times.

Evolution does not lead to perfection

Mutations are random, it can take several mutations to lead to new traits, the trait my be beneficial, harmful, or neutral, depending on the environmental pressures at the moment, evolution is change in organisms over time (individuals do not evolve)

Shared ancestral character

found in common ancestor of taxa, and all members of the clade have it (some may have secondarily lost it), used to identify membership to the larger group (all decended from the same common ancestor)

Shared derived character (synapomorphy)

Within the larger clade, distinguishes those that share it, from those that do not, provides information about relatedness within the larger group, and used to identify branch points (nodes) within clade

Rule of Parsimony

Choose the simplest cladogram with fewest steps or events

Biological species concept

Defines species as groups of interbreeding populations that are reproductively isolated, and restricted definition to those organisms that undergo sexual reproduction

Phylogenetic species concept

Species is a population or set of populations characterized by one or more shared derived characters

Horizontal gene transfer

Transfer of genetic material between unrelated species - more prevalent in eukaryotes

Transformation

Naked DNA uptake by bacteria (absorption)

Transduction

Genes transferred by virus

Conjugation

Genes transferred between bacteria via pilus

Ring of Life model

Proposed that all three domains evolved from a pool of prokaryotes swapping genes through horizontal gene transfer