1. Systematics and the Phylogenetic Revolution
Chapter 23

2. Introduction All organisms: Are composed of one or more cells
Carry out metabolism
Transfer energy with ATP
Encode hereditary information in DNA
Tremendous diversity of life
Bacteria-----whales----sequoia trees
Biologists group organisms based on shared characteristics

3. Systematics
Since fossil records are not complete, scientists rely on other types of evidence to establish the best hypothesis of evolutionary relationships
Systematics: the study of evolutionary relationships
Phylogeny: a hypothesis about patterns of relationship among species

4. Systematics
Darwin envisioned that all species were descended from a single common ancestor
He depicted this history of life as a branching tree.
Now called a cladogram

5. Systematics Twigs of a tree represent existing species
Joining of twigs and branches reflects the pattern of common ancestry back in time to a single common ancestor
Darwin called this process “descent with modification”

6. Phylogenies depict evolutionary relationships
Systematics
Phylogenies depict evolutionary relationships

7. Systematics
Key to interpreting a phylogeny: look at how recently species share a common ancestor
Similarity may not accurately predict evolutionary relationships
Early systematists relied on the expectation that the greater the time since two species diverged from a common ancestor, more different would be

8. Systematics
Evolution can occur rapidly at one time and slowly at another (punctuated and gradual evolution)

9. Systematics
Oscillating selection: Traits can evolve in one direction, then back the other way
Evolution is not always divergent: convergent evolution
Use similar habitats
Similar environmental pressures
Evolutionary reversal: process in which a species re-evolves the characteristics of an ancestral species

10. Cladistics
Derived characteristic: similarity that is inherited from the most recent common ancestor of an entire group
Ancestral: similarity that arose prior to the common ancestor of the group
In cladistics, only shared derived characters are considered informative about evolutionary relationships
To use the cladistic method character variation must be identified as ancestral or derived

11. Cladistics Characters can be any aspect of the phenotype
Morphology - Physiology
Behavior - DNA
Characters should exist in recognizable character states
Example: Teeth in amniote vertebrates has two states, present in most mammals and reptiles and absence in birds and turtles

12. Cladistics Examples of ancestral versus derived characters
Presence of hair is a shared derived feature of mammals
Presence of lungs in mammals is an ancestral feature; also present in amphibians and reptiles

13. Cladistics Determination of ancestral versus derived
First step in a manual cladistic analysis is to polarize the characters (are they ancestral or derived)
Example: polarize “teeth” means to determine presence or absence in the most recent common ancestor

14. Cladistics Outgroup comparison is used to assign character polarity
A species or group of species not a member of the group under study is designated as the outgroup
Outgroup species do not always exhibit the ancestral condition

15. Cladistics
When the group under study exhibits multiple character states, and one of those states is exhibited by the outgroup, then that state is ancestral and other states are derived
Most reliable if character state is exhibited by several different outgroups

16. Cladistics Following the character state-outgroup method
Presence of teeth in mammals and reptiles is ancestral
Absence of teeth in birds and turtles is derived

17. Cladistics Construction of a cladogram Polarize characteristics
Clade: species that share a common ancestor as indicated by the possession of shared derived characters
Clades are evolutionary units and refer to a common ancestor and all descendants
Synapomorphy: a derived character shared by clade members

18. Cladistics A simple cladogram is a nested set of clades
Plesiomorphies: ancestral states
Symplesiomorphies: shared ancestral states

20. Cladistics

21. Cladistics
Homoplasy: a shared character state that has not been inherited from a common ancestor
Results from convergent evolution
Results from evolutionary reversal
If there are conflicts among characters, use the principle of parsimony which favors the hypothesis that requires the fewest assumptions

22. Parsimony and Homoplasy
Cladistics
Parsimony and Homoplasy

23. Cladistics
A Cladogram; DNA

24. Cladistics
A Cladogram: DNA

25. Other Phylogenetic Methods
Some characters evolve rapidly and principle of parsimony may be misleading
Rate at which some parts of the DNA genome evolve
Mutations in repetition sequences, not deleted by natural selection
Statistical approaches
Molecular clock: rate of evolution of a molecule is constant through time

26. Systematics and Classification
Classification: how we place species and higher groups into the taxonomic hierarchy
Genus, family, class..
Monophyletic group: includes the most recent common ancestor of the group and all of its descendants (clade)
Paraphyletic group: includes the most recent common ancestor of the group, but not all its descendants

27. Systematics and Classification
Polyphyletic group: does not include the most recent common ancestor of all members of the group
Taxonomic hierarchies are based on shared traits, should reflect evolutionary relationships
Why should you refer to birds as a type of dinosaur?

28. Systematics and Classification
Monophyletic Group

29. Systematics and Classification
Paraphyletic Group

30. Systematics and Classification
Polyphyletic Group

31. Systematics and Classification
Old plant classification system

32. Systematics and Classification
New plant classification system

33. Systematics and Classification
Phylogenetic species concept (PSC)
Focuses on shared derived characters
Biological species concept (BSC)
Defines species as groups of interbreeding population that are reproductively isolated
Phylogenetic species concept: species should be applied to groups of populations that have been evolving independently of other groups

34. Systematics and Classification
BSC cannot be applied to allopatric populations
PSC can be applied to allopatric populations
PSC can be applied to both sexual and asexual species
BSC can be applied only to sexual species
PSC still controversial

35. Systematics and Classification
Paraphyly and phylogenetic species concept

36. Comparative Biology
Phylogenetics is the basis of all comparative biology
Homologous structures are derived from the same ancestral source (e.g. dolphin flipper and horse leg)
Homoplastic structures are not (e.g. wings of birds and dragonflies):
-Parental care
Dinosaurs, birds, crocodiles
Homologous behavior

37. Parental care in dinosaurs and crocodiles
Comparative Biology
Parental care in dinosaurs and crocodiles

38. Comparative Biology Homoplastic convergence: saber teeth
Occurred in different groups of extinct carnivores
Similar body proportions (cat)
Similar predatory lifestyle
Most likely evolved independently at least 3 times

39. Distribution of saber-toothed mammals
Comparative Biology
Distribution of saber-toothed mammals

40. Comparative Biology Homoplastic convergence: plant conducting tubes
Sieve tubes facilitate long-distance transport of food that is essential for the survival of tall plants
Brown algae also have sieve elements
Closest ancestor a single-celled organism

41. Convergent evolution of conducting tubes
Comparative Biology
Convergent evolution of conducting tubes

43. Comparative Biology
Most complex characters evolve through a sequence of evolutionary changes
Modern-day birds
wings, feathers, light bones, breastbone
Initial stages of a character evolved as an adaptation to some environmental selective pressure
First featherlike structure evolved in theropod phylogeny
Insulation or perhaps decoration

44. Comparative Biology

45. Comparative Biology
Phylogenetic methods can be used to distinguish between competing hypotheses
Larval dispersal in marine snails
Some snails produce microscopic larvae that drift in the ocean currents
Some species have larvae that settle to the ocean bottom and do not disperse
Fossils show increase in nondispersing snails

46. Comparative Biology
Increase through time in proportion of species whose larvae do not disperse

47. Comparative Biology
Two processes could produce an increase in nondispersing larvae
Evolutionary change from dispersing to nondispersing occurs more often than change in the opposite direction
Species that are nondispersing speciate more frequently, or become extinct less frequently than dispersing species
The two processes would result in different phylogenetic patterns

48. Comparative Biology

49. Comparative Biology Analysis indicates:
Evolutionary increase in nondispersing larvae through time may be a result of both a bias in the evolutionary direction and an increase in rate of diversification
Lack of evolutionary reversal

50. Comparative Biology Loss of larval stage in marine invertebrates
Nonreversible evolutionary change
Marine limpets: show direct development has evolved many times
3 cases where evolution reversed and larval stage re-evolved

51. Comparative Biology

52. Comparative Biology
Phylogenetics helps explain species diversification
Use phylogenetic analysis to suggest and test hypotheses
Species richness in beetles
Coleoptera: 60% of all animals are insects and 80% of all insects are beetles
Phytophaga: clade with most herbivorous beetles
Family Nemonychidae: specialized on conifers since Jurassic

53. Evolutionary diversification of the Phytophaga
Comparative Biology
Evolutionary diversification of the Phytophaga

54. Comparative Biology
Phylogenetic explanations for beetle diversification
Not the evolution of herbivory
Specialization on angiosperms a prerequisite for diversification
Risen 5 times independently within herbivorous beetles
Angiosperm specializing clade is more species-rich than the clade most closely related

55. Disease Evolution
HIV evolved from a simian (monkey) viral counterpart SIV
First recognized in 1980’s
Current estimate: >39 million people infected; > 3 million die each year
SIV found in 36 species of primates
Does not usually cause illness in monkeys
Around for more than a million years as SIV

56. Disease Evolution

57. Disease Evolution Phylogenetic analysis of HIV and SIV
First: HIV descended from SIV
All strains of HIV are nested within clades of SIV
Second: a number of different strains of HIV exits
Independent transfers from different primate species
Each human strain is more closely related to a strain of SIV than to other HIV strains

58. Disease Evolution
Third: humans have acquired HIV from different host species