1. Phylogeny and Systematics
Chapter 25 or 26 (Depending on Version of Campbell)

2. Terminology
Phylogeny: the evolutionary history of a group of organisms
Evidence used to reconstruct phylogenies can be obtained from the fossil record and from morphological and biochemical similarities between organisms
Systematics: an analytical approach to understanding the diversity and relationships of living and extinct organisms.
Molecular systematics: uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships

3. Classification

4. Diversity of Life
Biologists have identified over 1.5 million different species of living organisms so far . . .
Estimates = between million species yet to be discovered

6. What is Classification?
Classification is the systematic grouping of living organisms based on characteristics, hierarchical or evolutionary relationships
Classification is also known as taxonomy
Taxonomists are scientists that identify and name organisms
Carolus Linnaeus – 1748 – developed classification scheme for all plants and animals known at the time
Linnaeus’s classification was based on resemblances between organisms

7. Standardized Naming Binomial nomenclature used Genus species
Latin or Greek
Italicized in print
Capitalize genus, but NOT species
Turdus migratorius
American Robin

8. Binomial Nomenclature
The polar bear- Ursus maritimus.
Ursus—is the genus to which the organism belongs.
A genus is a group of similar species. The genus Ursus contains five other species of bears, including Ursus arctos, the brown bear or grizzly bear.
The second part of a scientific name (species) —maritimus for polar bears—is unique to each species and is a description of the organism’s habitat/important trait. The Latin word maritimus refers to the sea: polar bears often live on pack ice that floats in the sea.
Which TWO are more closely related?

9. Classification Groups
Taxon (taxa – plural) is a category into which related organisms are placed
There is a hierarchy of groups (taxa) from broadest to most specific
Domain, Kingdom, Phylum, Class, Order Family, Genus, species

10. Dashing
King
Phillip
Came
Over
For
Good
Soup!

12. Cladograms

13. Taxons Most genera contain a number of similar species
The genus Homo is an exception (only contains modern humans)
Classification is based on evolutionary relationships

14. Basis for Modern Taxonomy
Modern taxonomy is grouping organisms based on their evolutionary history
Based on:
Homologous structures (same structure, diff. function)
Embryo development
Molecular similarity in DNA, RNA, amino acid sequences

15. Modern Taxonomy : Cladistics
Cladistics is a system of classifying organisms that considers only characteristics that are “new evolutionary innovations”
Characteristics that appear in recent parts of the lineage but not in its older members = derived characters

16. Cladogram
Derived characters can be used to construct a diagram that shows evolutionary relationships among groups of organisms

17. Using DNA to classify organisms
The more derived genetic characters two species share, the more recently they shared a common ancestor and the more closely they are related in evolutionary terms.

18. Reading Cladograms
Mark the organisms that have a molted external skeleton.
Use a different mark for the organisms without a molted external skeleton.
Circle the point on the cladogram that shows the most recent common ancestor of the crab and the barnacle.
Draw an X at the point on the cladogram that shows the most recent common ancestor of mollusks and crustaceans.
Which organism, or organisms, shows segmentation?
What do all three organisms have in common?

19. Lamprey Snapping Turtle Tuna
Kangaroo Mammal (Marsupial)
Lamprey
Agnatha
Rhesus Monkey Mammal (Placental)
Bullfrog Amphibian
Snapping Turtle
Reptile
Tuna
Fish (Osteichthyes)

22. Classification and phylogeny are linked
Systematists construct diagrams called phylogenetic trees to depict evolutionary relationships
The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups

23. What phylogenetic trees don’t tell us
The sequence of branching in a tree does not necessarily indicate the actual ages of the particular species
Tree shows most recent common ancestor
Tree does not show when a particular species evolved or how much genetic change occurred in each evolutionary lineage.

24. Phylogenies are inferred from morphological and molecular data
Similarities due to shared ancestry are called homologies.
Organisms that share similar morphologies or DNA sequences are likely to be more closely related than organisms without such similarities.

25. Homologies vs. Analogies
Similarity due to convergent evolution is called analogy.
When two organisms from different evolutionary lineages experience similar environmental pressures, natural selection may result in convergent evolution.
Similar analogous adaptations may evolve in such organisms.
Analogies are not due to shared ancestry.

27. Molecular Similarities
Systematists compare DNA to assess relationships between species
If genes in two organisms have closely similar nucleotide sequences, it is likely that the genes are homologous
It is necessary to distinguish homology from analogy to establish relationships.
Scientists have developed mathematical tools that can distinguish “distant” homologies from coincidental matches in divergent sequences.

28. Cladograms
Clade: a group of species that includes an ancestral species and all its descendants.
Study of relationships among clades = cladistics
Monophyletic clades: consists of an ancestral species and all its descendents
Paraphyletic clades: include some but not all of the descendents
Polyphyletic clades: groupings that lack a common ancestor

29. Cladograms
A “character” refers to any feature that ia particular taxon possesses.
A shared derived character is unique to a particular clade
A shared primitive character is found not only in the clade being analyzed but also in older clades
Examples: hair is a shared derived character of all mammals; back bone is a shared primitive character
Shared derived characters are useful in constructing cladogram
Shared primitive characters are not useful

30. Cladograms (continued)
A key step in cladistic analysis is outgroup comparison, which is used to differentiate shared primitive characters from shared derived ones.
Outgroup: a species or group that is closely related to the species being studied but known to be less closely related than any members of the study group are to each other.
Ingroup: related species being studied
Similarities between outgroup and ingroup are assumed to be primitive characters

31. Too Much Info?
Increased DNA data makes it difficult to determine best representative tree.
Scientists look for the simplest explanation consistent with the facts = maximum parsimony
Principle of maximum likelihood = given certain rules about how DNA changes occur over time, a tree should reflect the most likely sequence of evolutionary events.

32. Phylogenetic trees are hypotheses
The best hypothesis is the one that best fits all available data
Hypotheses may be modified as new evidence becomes available.
Strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as fossil evidence

34. Universal Tree of Life
The genetic code is universal in all forms of life
This infers that all living things have a common ancestor
Scientists are working to link all organisms into a universal tree of life
Current information indicates:
There are three domains: Bacteria, Archaea, Eukarya
The early history of these domains is not yet clear.
There were probably many interchanges of genes among organisms of different domains