Lecture #2 | Tree of Life

Common descent

Darwin hypothesis that all life, living or extinct has descended without interruptions from one or a few original forms

• key goal is to construct “tree of life”

Age of single-celled ancestor

Lived around 3-4 billion years ago

• all extant lineages are the same age

Sources of data for phylogenies

1. Fossils

   1. Issue: habitat vary, complicating fossilization. Some organisms fossilize worse than others

2. Living organisms

   1. Where most evolutionary past has arose from. We deduce the past from the present

Ancestors and ancestral traits are implicit to phylogenies

Uses for phylogenies

1. Infer evolutionary relationships

2. Reconstruct evolutionary origins and divergence of key traits

3. Trace human origins and migrations

4. Forensics and criminology

5. Deduce the sources and carriers of diseases

What does this tree show?

HIV 1 and 2 arose from SIV that infected sooty mangabeys and chimpanzees

• jumped twice to humans

Phylogenetic trees

Branching diagram that represents a hypothesis about the evolutionary history of a group of organisms

Root

Point that represents ancestral lineage

Branch tips

Represents the most recent descendants of that ancestor

Node

Represents a common ancestor and the divergence of two evolutionary lineages from that common ancestor (speciation)

Common ancestor

An ancestral organism that gave rise to two or more descendent lineages

MRCA

Most recent common ancestor

Clade/monophyletic group

Common ancestor and all descendants

Paraphyletic

Ancestor and some (but not all descendants)

Polyphyletic

Distantly related species but not most recent common ancestor

Sister taxa

Groups that share a common ancestor that is no shared by an other group

Taxon

A systematic unit or group to which organisms are assigned

ex: species

Characters

The variable features of an organism: multiple character states are used to infer phylogenies

• can be phenotypes or genotypes

Phenotypes

Morphological, physiological, behavioral, biochemical

Genotypes

Specific set of genes/DNA sequences possessed by an individual

Constructing a phylogenetic tree

1. Group species according to character states, can be used to infer common descent

2. Calculate similarity by number of shared character states

Useful traits in a phylogeny

Traits shared by some, but not all lineages and are derived from a common ancestor

• phylogenies reconstruct evolutionary history, not similarity

Certainty of phylogenies

Every tree built is a hypothesis, proposing a particular evolutionary sequence of events

• we can usually not know with 100% certainty what the true history is

• can use different methods to find the tree that fits the data the best

Maximum Parsimony

The best phylogenetic hypothesis is the one that postulates the fewest evolutionary changes

• used in the absence of other evidence

• fewest steps

5 General patterns of morphological evolution

1. Most features of organisms have been modified from preexisting features

2. Different traits/characters evolve at different rates

3. Evolution is often gradual

4. Homoplasy is common

5. Many lineages contain adaptive radiations

Homologous characters

Similar physical features in different organisms that share a common ancestor, but the features serve different functions

• related organisms have these characters

• most complex structures do not evolve de novo (from nothings), but are modified from ancestral traits

Tetrapod forelimb

An ancient, lobe fin that is a homologous structures that has been modified for many new uses including swimming, flying, running, digging, and manual manipulation

Mosaic evolution

Species dont evolve as a whole

• individual traits can evolve in a piecemeal fashion and at different rates

Conserved characters

Traits or structures that change little over evolutionary time

Evolution is often graudual

Evolutionary gradations are often observed

• pattern of incremental differenced between species are often observed

Homoplasy

Similarity in a specific trait/character without any shared ancestry

• ex: while birds and pterosaurs both have wings, they independently evolved in each species

is the result of convergent evolution

Convergence

Superficially similar features that have indecently evolved in separate lineages

ex: vertebrate vs. invertebrate eyes

• both have lens and retina, but are otherwise profoundly different

Adaptive radiation

Periods of rapid formation of new species whose adaptations allow them to fill different ecological roles

• radiations often occur when a species invades open and diverse habitats (islands)

• ex: Galapagos finches