1. Phylogeny and Systematics
Chapter 25
Phylogeny and Systematics

2. Figure 25.1 A dragonfly fossil from Brazil, more than 100 million years old

3. Figure 25.2 An unexpected family tree

4. Figure 25.3 Formation of sedimentary strata containing fossils
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

5. Grand Canyon

6. Volcanic eruption

7. Figure 25.4 A gallery of fossil types
(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

8. Figure 25.5 Convergent evolution of analogous burrowing characteristics

10. Figure 25.6 Aligning segments of DNA
1 C C A T C A G A G T C C
2 C C A T C A G A G T C C
G T A
Deletion
Insertion
1 C C A T C A A G T C C
2 C C A T G T A C A G A G T C C
1 C C A T C A A G T C C
2 C C A T G T A C A G A G T C C
1 Ancestral homologous DNA segments are identical as species 1 and species 2 begin to diverge from their common ancestor.
2 Deletion and insertion mutations shift what had been matching sequences in the two species.
3 Homologous regions (yellow) do not all align because of these mutations.
4 Homologous regions realign after a computer program adds gaps in sequence 1.

11. Figure 25.7 A molecular homoplasy
A C G G A T A G T C C A C T A G G C A C T A
T C A C C G A C A G G T C T T T G A C T A G
25 percent of bases the same and not closely related

12. Figure 25.8 Hierarchical classification
Panthera
pardus
Felidae
Carnivora
Mammalia
Chordata
Animalia
Eukarya
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

13. Figure 25.9 The connection between classification and phylogeny
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

14. Unnumbered Figure p.497
Leopard
Domestic cat
Common ancestor

15. Unnumbered Figure p.497
Leopard
Domestic cat
Common ancestor
Wolf

16. Figure 25.10 Monophyletic, paraphyletic, and polyphyletic groupings
(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.)
(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 E C G H F J K I B A
Grouping 2
Grouping 3
Grouping 1
(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.
Valid clad is monophyletic (single tribe)

17. Figure 25.11 Constructing a cladogram
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

18. Figure 25.12 Phylogram
Drosophila
Lancelet
Amphibian
Fish
Bird
Human
Rat
Mouse
Using the hedgehog genes -It plays a key role in regulating vertebrate organogenesis, such as in the growth of digits on limbs and organization of the brain

19. Figure 25.13 Ultrametric tree
Drosophila
Lancelet
Amphibian
Fish
Bird
Human
Rat
Mouse
Cenozoic
Mesozoic
Paleozoic
Proterozoic
542
251
65.5
Millions of
years ago

20. Figure 25.14 Trees with different likelihoods
Human
Tree 1: More likely
Mushroom
Tulip
40%
30%
(a) Percentage differences between sequences
(b) Comparison of possible trees
Tree 2: Less likely
15% 5%
20%
10%
25%

21. Figure 25.15 Applying Parsimony to a Problem in Molecular Systematics
APPLICATION In considering possible phylogenies for a group of species, systematists compare molecular data for the species. The most efficient way to study the various phylogenetic hypotheses is to begin by first considering the most parsimonious—that is, which hypothesis requires the fewest total evolutionary events (molecular changes) to have occurred.
TECHNIQUE Follow the numbered steps as we apply the principle of parsimony to a hypothetical phylogenetic problem involving four closely related bird species.
Species I
Species II
Species III
Species IV I II
III IV
Sites in DNA sequence
Three possible phylogenetic hypothese 1 2 3 4 5 6 7 A G T
Bases at site 1 for each species
Base-change event
1 First, draw the possible phylogenies for the species (only 3 of the 15 possible trees relating these four species are shown here).
2 Tabulate the molecular data for the species (in this simplified example, the data represent a DNA sequence consisting of just seven nucleotide bases).
3 Now focus on site 1 in the DNA sequence. A single base- change event, marked by the crossbar in the branch leading to species I, is sufficient to account for the site 1 data.
Species

22. I II
III IV GG AA T G
10 events
9 events
8 events
4 Continuing the comparison of bases at sites 2, 3, and 4 reveals that each of these possible trees requires a total of four base-change events (marked again by crossbars). Thus, the first four sites in this DNA sequence do not help us identify the most parsimonious tree.
5 After analyzing sites 5 and 6, we find that the first tree requires fewer evolutionary events than the other two trees (two base changes versus four). Note that in these diagrams, we assume that the common ancestor had GG at sites 5 and 6. But even if we started with an AA ancestor, the first tree still would require only two changes, while four changes would be required to make the other hypotheses work. Keep in mind that parsimony only considers the total number of events, not the particular nature of the events (how likely the particular base changes are to occur).
6 At site 7, the three trees also differ in the number of evolutionary events required to explain the DNA data.
RESULTS To identify the most parsimonious tree, we total all the base-change events noted in steps 3–6 (don’t forget to include the changes for site 1, on the facing page). We conclude that the first tree is the most parsimonious of these three possible phylogenies. (But now we must complete our search by investigating the 12 other possible trees.)
Two base
changes

23. Figure 25.16 Parsimony and the analogy-versus-homology pitfall
Lizard
Four-chambered heart
Bird
Mammal
(a) Mammal-bird clade
(b) Lizard-bird clade

24. Figure 25.17 Two types of homologous genes
Ancestral gene
Speciation
Orthologous genes
Gene duplication
Paralogous genes
(a)
(b)
Orthologous - diverge after speciation, beta hemoglobin of humans and mice
Paralogous - can diverge in the same evolutionary lineage, olfactory receptors

25. Speciation with divergence of gene
Fig a
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Figure How two types of homologous genes originate
Orthologous genes
Species A
Species B
(a) Orthologous genes

26. Gene duplication and divergence
Fig b
Species A
Gene duplication and divergence
Figure How two types of homologous genes originate
Paralogous genes
Species A after many generations
(b) Paralogous genes

27. Figure 25.18 The universal tree of life
Bacteria
Eukarya
Archaea
4 Symbiosis of chloroplast ancestor with ancestor of green plants
3 Symbiosis of mitochondrial ancestor with ancestor of eukaryotes
2 Possible fusion of bacterium and archaean, yielding ancestor of eukaryotic cells
1 Last common ancestor of all living things 4 3 2 1
Billion years ago
Origin of life