1. Phylogeny and Systematics
Chapter 25
Phylogeny and Systematics

2. Overview: Investigating the Tree of Life
This chapter describes how biologists trace phylogeny
The evolutionary history of a species or group of related species

3. Biologists draw on the fossil record
Which provides information about ancient organisms
Figure 25.1

4. Biologists also use systematics
As an analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct

5. Currently, systematists use
Morphological, biochemical, and molecular comparisons to infer evolutionary relationships
Figure 25.2

6. Concept 25.1: Phylogenies are based on common ancestries inferred from fossil, morphological, and molecular evidence

7. The Fossil Record Sedimentary rocks Are the richest source of fossils
Are deposited into layers called strata
1 Rivers carry sediment to the ocean. Sedimentary rock layers containing fossils form on the ocean floor.
2 Over time, new strata are deposited, containing fossils from each time period.
3 As sea levels change and the seafloor is pushed upward, sedimentary rocks are exposed. Erosion reveals strata and fossils.
Younger stratum with more recent fossils
Older stratum with older fossils
Figure 25.3

8. The fossil record Fossils reveal
Is based on the sequence in which fossils have accumulated in such strata
Fossils reveal
Ancestral characteristics that may have been lost over time

9. Though sedimentary fossils are the most common
Paleontologists study a wide variety of fossils
Figure 25.4a–g
(a) Dinosaur bones being excavated from sandstone
(g) Tusks of a 23,000-year-old mammoth, frozen whole in Siberian ice
(e) Boy standing in a 150-million-year-old dinosaur track in Colorado
(d) Casts of ammonites, about 375 million years old
(f) Insects preserved whole in amber
(b) Petrified tree in Arizona, about 190 million years old
(c) Leaf fossil, about 40 million years old

10. Morphological and Molecular Homologies
In addition to fossil organisms
Phylogenetic history can be inferred from certain morphological and molecular similarities among living organisms
In general, organisms that share very similar morphologies or similar DNA sequences
Are likely to be more closely related than organisms with vastly different structures or sequences

11. Sorting Homology from Analogy
A potential misconception in constructing a phylogeny
Is similarity due to convergent evolution, called analogy, rather than shared ancestry

12. Convergent evolution occurs when similar environmental pressures and natural selection
Produce similar (analogous) adaptations in organisms from different evolutionary lineages
Figure 25.5

13. Concept 25.2: Phylogenetic systematics connects classification with evolutionary history
Taxonomy
Is the ordered division of organisms into categories based on a set of characteristics used to assess similarities and differences

14. Binomial Nomenclature
Is the two-part format of the scientific name of an organism
Was developed by Carolus Linnaeus

15. The binomial name of an organism or scientific epithet
Is latinized
Is the genus and species

16. Hierarchical Classification
Linnaeus also introduced a system
For grouping species in increasingly broad categories
Panthera
pardus
Felidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Figure 25.8

17. Linking Classification and Phylogeny
Systematists depict evolutionary relationships
In branching phylogenetic trees
Panthera pardus (leopard)
Mephitis mephitis (striped skunk)
Lutra lutra (European otter)
Canis familiaris (domestic dog)
Canis lupus (wolf)
Panthera
Mephitis
Lutra
Canis
Felidae
Mustelidae
Canidae
Carnivora
Order
Family
Genus
Species
Figure 25.9

18. Each branch point Represents the divergence of two species Leopard
Domestic cat
Common ancestor

19. “Deeper” branch points
Represent progressively greater amounts of divergence
Leopard
Domestic cat
Common ancestor
Wolf

20. A clade within a cladogram
Concept 25.3: Phylogenetic systematics informs the construction of phylogenetic trees based on shared characteristics
A cladogram
Is a depiction of patterns of shared characteristics among taxa
A clade within a cladogram
Is defined as a group of species that includes an ancestral species and all its descendants
Cladistics
Is the study of resemblances among clades

21. Cladistics
Clades
Can be nested within larger clades, but not all groupings or organisms qualify as clades

22. A valid clade is monophyletic
Signifying that it consists of the ancestor species and all its descendants
(a) Monophyletic. In this tree, grouping 1, consisting of the seven species B–H, is a monophyletic group, or clade. A mono- phyletic group is made up of an ancestral species (species B in this case) and all of its descendant species. Only monophyletic groups qualify as legitimate taxa derived from cladistics.
Grouping 1 D C E G F B A J I K H
Figure 25.10a

23. A paraphyletic clade
Is a grouping that consists of an ancestral species and some, but not all, of the descendants
(b) Paraphyletic. Grouping 2 does not meet the cladistic criterion: It is paraphyletic, which means that it consists of an ancestor (A in this case) and some, but not all, of that ancestor’s descendants. (Grouping 2 includes the descendants I, J, and K, but excludes B–H, which also descended from A.) D C E B G H F J I K A
Grouping 2
Figure 25.10b

24. A polyphyletic grouping
Includes numerous types of organisms that lack a common ancestor
Grouping 3
(c) Polyphyletic. Grouping 3 also fails the cladistic test. It is polyphyletic, which means that it lacks the common ancestor of (A) the species in the group. Further- more, a valid taxon that includes the extant species G, H, J, and K would necessarily also contain D and E, which are also descended from A. D C B E G F H A J I K
Figure 25.10c

25. Shared Primitive and Shared Derived Characteristics
In cladistic analysis
Clades are defined by their evolutionary novelties

26. A shared primitive character
Is a homologous structure that predates the branching of a particular clade from other members of that clade
Is shared beyond the taxon we are trying to define

27. A shared derived character
Is an evolutionary novelty unique to a particular clade

28. Systematists use a method called outgroup comparison
Outgroups
Systematists use a method called outgroup comparison
To differentiate between shared derived and shared primitive characteristics

29. As a basis of comparison we need to designate an outgroup
which is a species or group of species that is closely related to the ingroup, the various species we are studying
Outgroup comparison
Is based on the assumption that homologies present in both the outgroup and ingroup must be primitive characters that predate the divergence of both groups from a common ancestor

30. The outgroup comparison
Enables us to focus on just those characters that were derived at the various branch points in the evolution of a clade
Salamander
TAXA
Turtle
Leopard
Tuna
Lamprey
Lancelet (outgroup) 1
Hair
Amniotic (shelled) egg
Four walking legs
Hinged jaws
Vertebral column (backbone)
Amniotic egg
Vertebral column
(a) Character table. A 0 indicates that a character is absent; a 1 indicates that a character is present.
(b) Cladogram. Analyzing the distribution of these derived characters can provide insight into vertebrate phylogeny.
CHARACTERS
Figure 25.11a, b

31. Phylogenetic Trees and Timing
Any chronology represented by the branching pattern of a phylogenetic tree
Is relative rather than absolute in terms of representing the timing of divergences

32. Phylograms In a phylogram
The length of a branch in a cladogram reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in that lineage
Drosophila
Lancelet
Amphibian
Fish
Bird
Human
Rat
Mouse
Figure 25.12

33. Ultrametric Trees In an ultrametric tree
The branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal length
Drosophila
Lancelet
Amphibian
Fish
Bird
Human
Rat
Mouse
Cenozoic
Mesozoic
Paleozoic
Proterozoic
542
251
65.5
Millions of
years ago
Figure 25.13

34. Maximum Parsimony and Maximum Likelihood
Systematists
Can never be sure of finding the single best tree in a large data set
Narrow the possibilities by applying the principles of maximum parsimony and maximum likelihood

35. Comparing nucleic acids or other molecules to infer relatedness
Concept 25.4: Much of an organism’s evolutionary history is documented in its genome
Comparing nucleic acids or other molecules to infer relatedness
Is a valuable tool for tracing organisms’ evolutionary history