1. Ch. 26 – Phylogeny and the Tree of Life
We can decide in which container to place a species by comparing its traits with those of potential close relatives
We will survey the diversity and describe hypotheses regarding how it evolved
Phylogeny
Systematics
Discipline focused on classifying organisms and determining their evolutionary relationships (phylogeny)

2. Phylogeny and Systematics
Taxonomy
Science of classification
Sort and identify closely related species
Specific group is a taxon
Binomial nomenclature
2 part Latin name
Genus, species

3. Phylogeny and Systematics
Hierarchical classification
Linnaeus’ 7 level scheme:
Kingdom
Phylum (Division for plants and fungi)
Class
Order
Family
Genus
Species
Domains are now above kingdoms
3 exist
Taxon
Toxonomic unit at any level of the hierarchy

4. Linking Classification and Phylogeny
Phylogenetic Tree
Diagram that displays evolutionary relationships
The sequence of branching symbolizes historical chronology.
The last ancestor common to both the cat and dog families lived longer ago than the last common ancestor shared by leopards and domestic cats.
PhyloCode
Resulted due to difficulties with the Linnean system
Only names groups that include a common ancestor of all its descendents
Ranks would no longer exist

5. Linking Classification and Phylogeny
Reading a phylogenetic tree
Branch points
Divergence
Sister taxa
Groups of organisms that share an immediate common ancestor
Rooted
Represents most common ancestor of all taxa in the tree
Basal Taxon
Lineage that diverges early in the history of a group
Polytomy
Branch point from which more than two descendent groups emerge

6. Phylogenetic Trees Intended to show patterns of descent
Sequence of branching in a tree does not necessarily indicate the actual (absolute) ages of the particular species
Don’t assume that a taxon evolved from the taxon next to it

7. Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.
Construct a cladogram based on the following traits (characters) in the character table
Fig

8. Fig

9. Morphological & Molecular Homologies
Homology
shared ancestry; causes likeness
Can vary in appearance but still not in the genes
Analogy
convergent evolution
acquisition of similar characteristics due to sharing similar ecological roles
External appearance very similar but internal anatomy, physiology, and reproductive systems are dissimilar
Homoplasies
Analagous structures that arise independently

10. Molecular Homologies Comparisons of DNA Molecular Systematics
Uses data from DNA and other molecules to determine evolutionary relationships

11. Cladistics
Common ancestry is the primary criterion used to classify organisms
Clades
Groups that include an ancestral species and all of its descendents
Monophyletic group
Paraphyletic group
Polyphyletic group

12. Cladistics Monophyletic group
Allows a taxon to be equivalent to a clade
Group of taxa that consists of an ancestor and all of its descendents
Paraphyletic group
Ancestral species and SOME of its descendents
Polyphyletic group
Taxa with 2 or more different ancestors

13. Shared Ancestral & Derived Characters
Shared Ancestral Character
Originated in an ancestor of the taxon
Backbone of mammals
Shared Derived Character
Evolutionary novelty unique to a clade
Hair in mammals

14. Inferring Phylogenies using Derived Characters
Outgroup
A species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (ingroup)
Evidence used for cladistics
Fossil record
Homology (morphology, embryology, reproduction)
DNA sequences
Biogeography
Direct observation

15. Gene Duplications & Gene Families
Two distinct types of homologous genes
Orthologous genes
Found in different species and their divergences traces back to the speciation events that produced the species
Paralogous genes
Multiple copies of genes have diverged from one another in a species

16. Molecular Clocks Molecular Clock
A yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates
Neutral Theory
Most evolutionary change has no effect on fitness

19. From Two Kingdoms to Three Domains
Plants and Animals
Five Kingdoms
Monera, Protista, Plantae, Fungi, Animalia
Prokaryotic v. Eukaryotic
Unicellular v. Multicellular
Autotrophic v. Heterotrophic
How does each kingdom classify?

20. From Two Kingdoms to Three Domains
Archaea
Bacteria
Eukarya
Six-Kingdom system
Eubacteria and Archaebacteria
Extreme halophiles
Thermoacidophiles
Methanogens

23. Alternatives to the 6 Kingdom System
Eight-Kingdom system - proposed
Protists split into 3 kingdoms
Fungal like, plant like, animal like
Still debate over splitting Archae and Eubacteria even further

24. Phylogeny Summarized (potential FR…hint, hint)
Evolutionary history of organisms
Base on principle of parsimony (simplest explanation is the best)
Mechanisms of speciation
Geographic (allopatric speciation)
Sympatric speciation
Reproductive isolation by prezygotic barriers
Reproductive isolation by postzygotic barriers
Investigating phylogeny (evidence, strengths, weaknesses)
Fossils
Anatomy/Morphology
Embryology
Molecular biology
Behavioral traits

25. Phylogeny Summarized (potential FR…hint, hint)
Mechanisms of speciation
Geographic (allopatric speciation)
Population of one species becomes physically separated by some geographic barrier such as a river, mountain range, etc.
Long term isolation will lead to reproductive isolation
Sympatric speciation
Occurs when new species arise as a result of reproductive isolation within the population range
ex – result of polyploidy or switching mating behaviors
Reproductive isolation by prezygotic barriers
Habitat, temporal, behavioral, mechanical or gamete incompatibility
Reproductive isolation by postzygotic barriers
Reduced hybrid variability or fertility leads to speciation

26. Phylogeny Summarized (potential FR…hint, hint)
Investigating phylogeny (evidence)
Fossils
(strength) Determine time, extinct species
(weakness) not all species leave fossils; incomplete chronicle
Anatomy/Morphology
(strength) homologous structures
(weakness) analogous structures, little diversity in taxa, morphology may reflect environment or diet
Embryology
(strength) similarities in patterns of development not present in adults
(weakness) similarities lost in later development (chordates)

27. Phylogeny Summarized (potential FR…hint, hint)
Investigating phylogeny (evidence)
Molecular Biology
(strength) Lots of traits to study closely related species; most accurate
(weakness) virtually no data for extinct species; variation within species blurs variation between species
Behavioral traits
(strength) genetic based (frog calls)
(weakness) culturally transmitted or learned (bird calls)