1. Reconstructing and using phylogenies
Chapter 16
Reconstructing and using phylogenies

2. 16.1 All of life is Connected through is Evolutionary History
Evolutionary biologists believe that all life is connected to a common ancestor
Phylogeny-the evolutionary history of a particular group of organisms or their genes
Phylogenetic tree-a diagram that shows the phylogenies of a group of organisms or their genes

3. Phylogenetic tree

4. The trees used to be constructed based on physical structures and behaviors
They are now created based on genes and are considered more accurate
A series of ancestor and descendant populations form a lineage (straight line)
When a lineage splits (speciation), it creates a node and each line is a new lineage

5. Phylogenetic tree
Node

6. May portray thee evolutionary history of all life forms, a group, closely related species, or the history of individuals, populations, or genes within a species
Common ancestor forms the root of the tree
Splits either show speciation events, gene duplication events, or transmission events

8. Taxon-any group of species that we designate with a name (ex
Taxon-any group of species that we designate with a name (ex. Vertebrates)
Any taxon that consists of all the evolutionary descendants of a common ancestor is a clade
Two species that are each other’s closest relatives are called Sister species
Any two clades that are each other’s closest relatives are sister clades

10. Phylogenetic trees are the basis of comparative biology
Biologists use phylogenies to make comparisons and predictions about shared traits across genes, populations, and species
There are tens of millions of species on earth, 1.8 million species classified
Phylogenetic analyses are constantly reviewed and revised

11. The phylogenetic tree of life allows us to make predictions about species that we have not studied in detail based on comparisons
Any features shared by two or more species that have been inherited from a common ancestor are said to be homologous
Examples: DNA sequences, protein structures, and anatomical structures
Vertebral column is homologous in all vertebrates

12. Homologies

13. Derived traits provide evidence of evolutionary relationships
Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait)
Derived traits that are shared are used as evidence of common ancestry in a group are called synapomorphies
Example the vertebral column

14. derived characteristic
primitive characteristic

15. Not all similar traits show relatedness
They can develop in other ways:
1. Convergent evolution-Independent evolution of similar features from different ancestral traits
Example: wings of bats and birds are not homologous because they evolved independently from the forelimbs of different nonflying ancestors

16. Convergent Evolution vs. Divergent Evolution
Convergent: same traits evolved in unrelated species

17. 2. evolutionary reversal-when a character reverts from a derived state back to an ancestral state
Example: the fins of dolphins and whales

19. Similar traits generated by convergent evolution and evolutionary reversals are called homoplastic traits or homoplasies

20. 16.2 Phylogeny can be reconstructed from traits of organisms
In a phylogenetic study, the group of organisms of primary interest is called the ingroup
Which is compared to the outgroup which is a species or group known to be closely related to but phylogenetically outside the group of interest
The outgroup is used to determine which traits of the ingroup are derived and which are ancestral (figure 16.3)

21. Outgroup vs ingroup

22. Read page 319 & 320

23. Parsimony provides the simplest explanation for phylogenetic data
Parsimony principle-the preferred explanation of observed data is the simplest explanation
The best hypothesis under the parsimony principle is one that requires the fewest evolutionary changes (homoplasies)
Phylogenetic trees represent scientist’s best estimates about evolutionary relationships, given the evidence available
Modified a lot when new evidence arises

24. Hypothesis 1 is correct in accordance with the parsimony principle

25. Parsimony= simplest explanation is the most likely (Occam’s razor)– fewest evolutionary events is most likely

26. Phylogenies are reconstructed from many sources of data
Any trait that is genetically determined can be used in a phylogenetic analysis
Evolutionary relationships can be revealed through studies of morphology, development, the fossil record, behavioral traits, and molecular traits such as DNA and protein sequences

27. Morphology
Morphology-the presence, size, shape, and other attributes of body parts
Morphology still provides the most comprehensive data set available for many taxa
Morphological features are usually specific to certain groups (example floral organs for flowering plants)

29. Extinct phylogenies are almost all done by morphological data
The fossil record shows important data about ancestral traits and derived traits
The fossil record also show when lineages diverged
It is limited because some groups have few or no fossils and in some cases it is fragmented

31. Problems with morphology
Some taxa a morphologically very similar even though they are a very different species (example leopard frogs)
Few morphological traits can be compared across distantly related species
Morphological differences can be environmental and not genetic
Need more data

32. Development
Developmental patterns may reveal evolutionary relationships
Some organisms exhibit similarities in early developmental stages only
Example: notochord

34. Behavior
Some behavioral traits are culturally transmitted, others have a genetic basis
Bird songs, are often learned and may be inappropriate traits for phylogenies
Frog calls are genetically determined and are acceptable for phylogenies

35. Molecular Data
DNA sequences have become the most widely used sources of data for constructing trees
Look at mitochondrial DNA and cytoplasmic DNA as well
Also use nuclear gene sequences and amino acid sequences of proteins

36. Table 22.1 Molecular Data and the Evolutionary Relationships of Vertebrates

37. Biochemical Differences

38. Mathematical models expand the power of phylogenetic reconstruction
Maximum likelihood-method that will identify the tree that most likely produced the observed data, given the assumed model of evolutionary change
Most often used with molecular data
Incorporate more info about evolutionary change than parsimony methods
The disadvantage is that they are difficult to do and require in-depth models of evolutionary change

40. 16.4 Phylogeny is the basis of biological classification
The classification system that we use today was created in the 1700’s by Carolus Linnaeus
It is called Bionomial Nomenclature, gives each species two names
One identifies the genus (group closely related to species) and one identifies the species
Example Homo sapiens (Genus species)
Species name is underlined or in italics.
First letter in genus is capitalized

41. http://www. tutorvista

42. Sometimes abbreviated (ex. C. lupus)
Any group of organisms that is treated as a unit in classification is called a taxon
Kingdom>Phylum>Class>Order>Family>Genus>Species
Biologists today recognize the tree of life for biological classification
Use evolutionary relationships as the basis for classifying organisms. (do not always use Linnaean groups)

43. Taxonomy Hierarchy

44. Evolutionary history is the basis for modern biological classification
Taxa are expected to be monophyletic-the taxon contain an ancestor and all descendants of that ancestor, and no other organisms
Also the definition of a clade
Monophyletic group is a historical group of related species, or a complete branch on the tree of life

45. Monophyletic

46. Many mono- groups on a tree and these groups are smaller subset of larger mono- groups
A group that does not include its common ancestor is polyphyletic
A group that does not include all the descendants of a common ancestor is referred to as paraphyletic
These groups are inappropriate taxonomic units because they do not reflect evolutionary history. These are now being eliminated

47. Polyphyletic and paraphyletic

48. Several codes of biological nomenclature govern the use of scientific names
Biologists follow rules around the world so they can communicate about classification
Common names are not good because their could be many for one species or refer to more than one species
One rule is that each scientific name should be unique to a species

50. Phylogeny Video

51. Modern classifications are based on phylogenetic trees
(Linnaeus is dead)
Another important point is that modern classifications are based on phylogeny. 51

52. Linnaean Hierarchy Kingdom Animalia Phylum Chordata
Class Chondrichthyes
Class Osteichthyes
Class Amphibia
Class Reptilia
Class Aves
Class Mammalia
Traditional Linnaean classifications had a limited number of hierarchical levels—King Phillip chooses officer from good soldiers.
If we applied this to our phylogenetic tree of vertebrates, we would have only three levels… 52

53. However, modern classifications recognize groups of organisms by common ancestry.53

54. Trees and Classification
Clade: Mammals
That is, any group defined by a common ancestor—as shown here is called a clade, and can be recognized with a taxonomic name. 54

55. Trees and Classification
Clade: Amniotes
Likewise, more inclusive groups can be recognized. 55

56. Trees and Classification
Clade: Tetrapods
And this. In theory, there is no limit to how many of these groups could be recognized in a classification. 56

57. Classification Phylogeny Jawed vertebrates Bony vertebrates Tetrapods
Amniotes
Mammals
Archosaurs
In the case of our vertebrates, a phylogenetic classification might recognize six groups at five hierarchical levels. 57

58. Trees and Classification
Not a clade: Fish
The only limitation is that groups that contain some, but not all descendants of a common ancestor cannot be recognized. For instance, the common term “fish” has no phylogenetic meaning. We would call sharks and angelfish “fish”, but they are not a clade because their common ancestor down here also evolved into all these other forms. Another classic grouping that can no longer be recognized is the “reptilia”, because some reptiles like alligators are closer to birds than to other reptiles. 58

59. “…just as beginning students in geography need to be taught how to read maps, so beginning students in biology should be taught how to read trees and to understand what trees communicate.”
O’Hara Zoologica Scripta 26:323
More importantly than the fact that study of phylogenetic trees addresses federal and state science standards is that understanding trees is now fundamental for all biologists, not just those studying evolution. This is reflected in this quotation…
Phylogenetic trees are fundamental tools for organizing and interpreting all sorts of biological data. 59