BIOL 2410: Chapter 26 Lecture Notes

Phylogeny and the tree of life

Previous focus was on process – how things evolve

Next focus is on patterns of evolution

• Phylogeny is the evolutionary history of a species or group of related

species

• Systematics classifies organisms and determines their evolutionary

relationships

• Systematists use fossil, molecular, and genetic data to infer evolutionary

relationships

How do we know how things are related?

Go back and construct a reptile and snake phylogeny

Concept 26.1: Phylogenies show evolutionary relationships

Linnaeus: Binomial nomenclature: Genus species

Organisms share homologous characteristics because of common ancestry

• Taxonomy is the ordered division and naming of organisms

• Hierarchical Classification

• Kingdom, Phylum, Class, Order Family, Genus Species

Phylogenies reveal relationships

Phylogenetic tree is a hypothesis about Evolutionary relationship

Descended from common ancestor

Groups include an ancestor and all descendants

 • Each branch point represents the divergence of two species

• Sister taxa are groups that share an immediate common ancestor

• A rooted tree includes a branch to represent the last common ancestor of

all taxa in the tree

• A polytomy is a branch from which more than two groups emerge

Applying Phylogenies

Conservation:

Identify clades undergoing rapid diversification/extinction

Asses contribution of each to overall genetic diversity

Asses allele frequencies – identify evolutionary significant population units

or areas

Provide information on population connectivity over evolutionary time

Provide information for managing declining or threatened species

Examples: Conservation biology

• Determine source of illegal whale meat

• Red-cockaded Woodpecker:
o Loss of Critical Habitat
o Separated populations
o Move individuals from different population
o Differences between hatchery fish and wild fish
• Differences between wild and captive-bred populations

Concept 26.2: Phylogenies are inferred from morphological and molecular data

Molecular and morphological homologies

Homology – similarity due to shared common ancestor

 Analogy – Similarity due to convergent evolution

• Convergent evolution occurs when similar environmental pressures and

natural selection produce similar (analogous) adaptations in organisms
from different evolutionary lineages

• Wings are analogous

• Homologous as forearms

• Can also have molecular homologies

Fossil and molecular data used to distinguish analogy from homology

Evaluating molecular homologies

• Computers and mathematics help determine trees

• Computers aid in aligning sequences of different lengths

• Molecular systematics uses DNA and other molecular data to determine

evolutionary relationships

Concept 26.3: Shared characters are used to construct phylogenetic trees

Homologous characters used to construct a phylogeny

• Cladistics groups organisms by common descent

• A clade is a group of species that includes an ancestral species and all its
descendants

• A valid clade is monophyletic, signifying that it consists of the ancestor

species and all its descendants

• A paraphyletic grouping consists of an ancestral species and some, but not

all, of the descendants

• A polyphyletic grouping consists of various species that lack a common

ancestor
Shared Ancestral and Shared Derived Characters

An organisms has both shared and different characteristics

• A shared ancestral character is a character that originated in an ancestor of

the taxon

• A shared derived character is an evolutionary novelty unique to a particular

clade

• A character can be both ancestral and derived, depending on the context

• When inferring evolutionary relationships, it is useful to know in which

clade a shared derived character first appeared

Inferring phylogenies using derived characters

• An outgroup is a species or group of species that is closely related to the

ingroup, the various species being studied

• Outgroups have diverged from the lineage under study

• Systematists compare each ingroup species with the outgroup to

differentiate between shared derived and shared ancestral characteristics

• Homologies shared by the outgroup and ingroup are ancestral characters

that predate the divergence of both groups from a common ancestor

Phylogenetic Trees with Proportional Branch Lengths

Branch length = number of genetic changes

Maximum Parsimony and Maximum Likelihood

Use mathematics and computers to determine the best phylogenetic

relationships

Two methods are used:

 Parsimony: requires the fewest evolutionary changes

Maximum likelihood: Most likely sequence of evolutionary events

This method is often favored by current evolutionary biologist

Phylogenetic trees as Hypothesis

• The best hypotheses for phylogenetic trees fit the most data:
morphological, molecular, and fossil

• Phylogenetic bracketing allows us to predict features of an ancestor from

features of its descendents

• Birds, dinosaurs and crocodiles come from a common ancestor that brood
their eggs, sing for mates, and have a four chambered heart.

26.4 An organism’s evolutionary history is documented in its genome

• Molecular techniques help understand evolutionary relationships that

cannot be determined by comparative anatomy
o Relationships between animals and fungi
o Relationships of modern day prokaryotes and other microorganisms
• Different genes evolve at different rates
o rRNA change very slowly
o mtDNA evolves rapidly

Gene duplication and gene families

• gene duplication increases the number of genes

• provides more opportunity for evolutionary change
• repeated gene duplication results on gene families
o orthologous genes are homologous genes found in different species
o Paralogous genes are homologous genes result from gene
duplication and have more than one copy in the same genome
 Olfactory genes

Genome evolution
 • Orthologous genes are widespread
o 99% of human and mice genes are orthologous
o The number of genes have not duplicated at the same rate asa
phenotypic complexity
o Complex metazoans have genome complexity

26.5 Molecular clocks help track evolutionary time

Molecular Clock

To extend molecular phylogenies beyond the fossil record, we must make an

assumption about how change occurs over time

• A molecular clock uses constant rates of evolution in some genes to

estimate the absolute time of evolutionary change

Recent advances – three domain systems