1. Lecture V
How to Determine Evolutionary Relationships: Concepts in Phylogeny and Systematics
Textbook Reading: pp , in chapter 23: Reconstructing and using Phylogenies

2. Nature 413, (2001) Skeletons of terrestrial cetaceans and the relationship of whales to artiodactyls. J. G. M. Thewissen, E. M. Williams, L. J. Roe & S. T. Hussain. See webpage for link to pdf of this paper, and summary/persptive of this paper

4. Taxonomic classification is hierarchical and nested
Taxonomy is the science of the classification (=naming) of organisms
Linnean classification called binomial nomenclature, in reference to genus and specific epithet
Taxon is a generic term for any taxonomic unit (level)
Most inclusive taxon, not shown here, is Domain

5. Bass Frog Snake Bird “Basal” lineage
Phylogeny history of descent of a group of organisms from their common ancestor
Phylogenetic Tree or Cladogram. Depiction of a phylogeny. Carries information only on branching relationships; no information about passage of time or amount of phenotypic change. Each branching point (node) reflects a divergence (ie, speciation, cladogenesis) event that took place in the species that is the most recent common ancestor to the descendents of that cladogenesis event
Lineage Organisms in an ancestor-descendent relationship

6. Bass Frog Snake Bird Tunicate
Vertebrata (fish, amphibians,reptiles, birds)
Tetrapoda (frog, snake, bird)
Amniota (snake, bird)
Bass
Frog
Snake
Bird
Tunicate
The nested polygons here show taxonomic groupings, but with no regard for “inclusion” or “exclusion” of ancestors common to the groupings

7. Tunicate Bass Frog Snake Bird Amniota Tetrapoda Vertebrata
The nested polygons here do show taxonomic groupings, but with regard for “inclusion” or “exclusion” of ancestors common to the groupings

8. Determining monophyletic taxa is key to classifying organisms according to their evolutionary history:
Monophyletic taxon is one in which a single ancestor gives rise to all species, and which includes all descendents of that single ancestor
Paraphyletic taxon excludes one or more species descended from the most recent common ancestor of the taxon
Polyphyletic taxon excludes the most recent common ancestor of all members of the taxon
A taxon that includes only A and B would be paraphyletic
A taxon that includes B, C and D would be polyphyletic
A taxon that includes D, E and F would be monophyletic

9. “SCHOOLS” OF SYSTEMATICS
TRADITIONAL EVOLUTIONARY TAXONOMY [Simpson and others]
Establish taxa based on common ancestry (clades) and the extent of adaptive evolutionary change:
evolutionary groups that represent adaptive zone constitute legitimate higher taxa -- a grade
adaptive zone; “…characteristic reaction and mutual relationship between environment and organism, a way of life and not a place where life is led.”
paraphyletic taxa may be acceptable
PHYLOGENETIC SYSTEMATICS (CLADISTICS) [Hennig]
Establish taxa based on clades; monophyletic taxa only
Powerful methodological and analytic tool for determining relationships
The tools of cladistics now represent the prevailing approach to determining relationships; the philosophy of strict monophyly wrt classification is still under debate -- bears on definition - concept- of species
George Gaylord Simpson ( ). Mammalian Paleontologist, regarded as one of the architects of the modern synthesis. Formulated the principles of evolutionary taxonomy
Willi Hennig ( ). Hennig is best known for developing phylogenetic systematics, a coherent theory of the investigation and presentation of the relations that exist among species.

12. Systematists classify organisms and determine evolutionary relationships based on analysis of homologous characters (traits)
Systematic investigation is based on analysis of homologous characters (traits); characters may be morphological, molecular, behavioral, physiological..
Homologous character; character that is shared by two or more taxa because those taxa inherited the character from a common ancestor
Expect shared character to be quite similar, perhaps, but not identical among taxa, as a result of descent with modification
Homology indicates common ancestry, which is information with which one can determine evolutionary history
Divergent Evolution of Homologous Characters Homologous characters may “evolve away” from each other in structure

13. Aardvark, native to central, southern and eastern Africa
Analagous character; character occurring in two or more lineages because it evolved independently in each of those lineages,
Analagies may arise through convergent evolution: lineages occupy similar ecological roles and similar selective forces
Misinterpretation of analagous characters for homologus ones may lead to erroneous conclusions regarding phylogenetic relationships and unintended taxanomic groupings
Giant Anteater (at a termite mound), native to Latin America from Southern Mexico to Northern Argentina
Aardvark, native to central, southern and eastern Africa
Pangolin, native to Africa and southern and southeastern Asia
Convergent Evolution of Analogous Characters. Three distantly related mammals have structural similarities (analogous characters, homoplasious characters) due to convergent evolution. Each taxon independently evolved morphological traits for feeding on ants and termites.

14. The supporting structures of bird and bat wings are homologous structures; derived from a common ancestor
The supporting structures of insect wings are analogous to the structures of bird and bat wings; evolved independently.

15. Thorn of downy hawthorn is a modified stem
Spine develops from midrib of leaf
Shoot develops from axillary bud
Thorn develops from axillary bud
Thorn of downy hawthorn is a modified stem
Spine of Japanese barberry is a modified leaf
Analagous traits, or homoplasies, in two distantly related plant taxa

16. Phylogenetic Systematics Dr. Willi Hennig (1913-1976)
The history of diversification is recorded through descent with modification
Modification exists in the form of evolutionary transformation of characters from one state to another state.
Plesiomorphy: Ancestral character state
Apomorphy: Derived character state
Synapomorphy Derived character state that is exclusively shared by a subset of taxa under investigation.
A synapomorphy is evidence that taxa bearing it are descended from the same common ancestor -- the ancestor in which the derived character arose.
“Cladistic” or “Phylogenetic” Analysis: Procedural Outline
SELECT ORGANISMS
Identify the ingroup
Select an appropriate outgroup
BUILD TRANSFORMATION MATIX
Select characters for analysis
Assign character states
Determine polarity of character states
ANALYZE AND INTERPRET DATA
Subject data to optimization algorithm
(usually parsimony criteria) to produce an optimal tree, perhaps a concensus tree
Seek congruence
Product: Phylogenetic Hypothesis

17. Phylogenetic Systematics Dr. Willi Hennig (1913-1976)
The history of diversification is recorded through descent with modification
Modification exists in the form of evolutionary transformation of characters from one state to another state.
Plesiomorphy: Ancestral character state
Apomorphy: Derived character state
Synapomorphy Derived character state that is exclusively shared by a subset of taxa under investigation.
A synapomorphy is evidence that taxa bearing it are descended from the same common ancestor -- the ancestor in which the derived character arose.
“Cladistic” or “Phylogenetic” Analysis: Procedural Outline
SELECT ORGANISMS
Identify the ingroup
Select an appropriate outgroup
BUILD TRANSFORMATION MATIX
Select characters for analysis
Assign character states
Determine polarity of character states
ANALYZE AND INTERPRET DATA
Subject data to optimization algorithm
(usually parsimony criteria) to produce an optimal tree, perhaps a concensus tree
Seek congruence
Product: Phylogenetic Hypothesis

18. Species A Species B Species C
Reconstruct the phylogeny of three closely related bird species
Species A Species B Species C
Determine characters to use for analysis
bill shape (derived character state: hooked; ancestral= not hooked)
head feathers (derived = crest; ancestral = no crest)
toe condition (derived = webbed; ancestral = no webbing)

19. Species A Species B Species C
Hooked Bill Hooked Bill No Hooked Bill
Crested Head No Crested Head Crested Head
Webbed Toes Webbed Toes No Webbed Toes
Character states variously arise in lineages.
Character states variously accumulate in lineages, in descendents of the ancestor in which the character states arose

20. A B C ?

21. Outgroup Closely related species that we know diverged from ancestral lineage before our three species of interest diverged
Ingroup

22. ? (ingroup) Outgroup Species A Species B Species C
Transformation Series
Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup)
Bill Shape Head Plumage Toe Condition
Outgroup H C W-
Species A H C W+
Species B H C W+
Species C H C W- ?
(ingroup)
H=hooked bill C=crest W=webbed toes
+=species has trait -=species lacks trait
Assume character state seen in outgroup is ancestral character state.

23. Choosing Among Competing Hypotheses: The Parsimony Principle
The Parsimony Principle holds that, all other things being equal, the hypothesis requiring the fewest number of evolutionary transformations has the highest likelihood of being the correct hypothesis

24. ? (ingroup) Outgroup Species A Species B Species C
Closely related species that diverged from ancestral lineage before our three species of interest diverged (outgroup)
(ingroup)
Bill Shape Head Plumage Toe Condition
Outgroup H C W-
Species A H C W+
Species B H C W+
Species C H C W-
Outgroup Species A Species B Species C
Transformation Series
Assume character state seen in outgroup is ancestral. W- C- H- H+ W+ C+
This phylogenetic hypothesis requires four evolutionary transformations to explain the distribution of character states among taxa under investigation
OG B A C
H- C- W H+ C- W H+ C+ W H- C+ W-
This phylogenetic hypothesis requires five evolutionary transformations to explain the distribution of character states among taxa under investigation

25. Evolutionary relationships may be determined through analysis of molecular characters; DNA, RNA and proteins
Molecular biology provides powerful tools for systematics
Nucleotide sequences and therefore amino acid sequences, are inherited; both undergo descent with modification following divergence of one lineage into two
Extent of sequence differences between taxa is an indicator, an estimator, of time since divergence from a common ancestor
DNA , RNA and proteins are used to classify organisms and determine evolutionary relationships

27. Phenotypic consequence of a point mutation - a substitution
Normal RBC’s and normal hemoglobin
Normal rbcs are disk shaped (light micrograph), each with millions of hB molecules that function in O2 transport. hB molecule consists of four polypeptides; first seven amino acids of one of the four are shown; this polypeptide has 146 amino acids. Left; sligh change in the primary structure of hemogloonin, an inherited substitution of one amino acid, causes sickle-cell disease. The substitution occurs in the number 6 position of the polypeptide. The abnormal hb molecules tend to crystalize, deforming some of the cells into a sickle shape. People with sickle cell have periodic sickle-cell crises, which occur when the angular cells clog tiny blood vessesls, impeding blood flow.
Sickled RBC’s and sickle-cell hemoglobin
Phenotypic consequence of a point mutation - a substitution

28. Molecules evolve at different rates, some, at constant rates
The constant rate at which cytochrome c has evolved raiseds the interesting question of whether other proteins also evolve at constant rates. As a rule of thumb, highly conserved proteins like hemoglobin or cyctochrome c provide the best molecular clocks, but all proteins for which data are available appear to accumulate changes over time. However, different proteins evolve at very different ra5ts, as can be seen in here. This graph presents estimates of the number of “accceptable” point mutations (that is, changes successfully incorporated into the protein) per 100 amino acids per million years.
The fastest rate of change appears to be in fibrinopeptides, while the most highly conserved protein is histone H4. Even faster rates of change are seen for pseudogenes, which are not transcribed, suggesting that molecular evolution proceeds more quickly when less constraind by selection.
Molecules evolve at different rates, some, at constant rates
Raven and Johnson 1999)

29. Hemoglobin Evolution Gene duplication Multigene Families
Evolution of molecular function
Tetrameric Human hemoglobin

30. Gene family
-two or more genes in a genome, identical or highly similar in nucleotide sequence
-descended from the same ancestral gene
Origin of gene families
-Repeated gene duplication from errors during DNA replication and recombination

31. Globin gene families are well-studied across taxa for sequence, structure and function
Hemoglobin multigene families in humans
Alpha globin family (on chr. 16)
Beta globin family (on chr. 13)
Hemoglobin families probably descended from a myoglobin-like ancestral gene

32. Evolutionary Time

33. Evolution of the Globin Gene
Genes encoding proteins have undergone continual evolution, accumulating increasing numbers of changes over time
Length of lines corresponds to number of nucleotide substitutions in the gene
Raven and Johnson 1999
Some genes such as the one coding for the protein hemoglobin, have been well studied and the entire time course of their evolution can be laid out with confidence by tracing the origin of particulr substittuions in their nucleotide sequencs
The pattern of descent obtained is called a phylogenetic tree. It represents tehe evoltuinary history of the gene. The successive changes in the hemoglobin molecule produce a tree that closely reflects the evolutionary relationships predicted by morphlogical charactrers. Whales, dolphins and porpoises cluster together, as do the primates and the hoofed animals. The patttern of accumulating changes seen in the moecular record consititutes strong direct evidence for macroevoltion