1. Chapter 21 Lecture and Animation Outline
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2. Darwin’s bark spider, Caerostris darwini, was discovered in 2010
Darwin’s bark spider, Caerostris darwini, was discovered in The female of this species weaves an enormous web.

3. Chapter 21 Taxonomy and Systematics
Chapter Outline:
Taxonomy
Phylogenetic Trees
Cladistics
Molecular Clocks
Horizontal Gene Transfer

4. Taxonomy Taxonomy Systematics
Science of describing, naming, and classifying living and extinct organisms
Systematics
Study of diversity and evolutionary relationships among organisms, both extinct and modern
Taxonomic groups are based on hypotheses regarding evolutionary relationships derived from systematics

5. Taxonomy Hierarchical system involving successive levels
Each group at any level is called a taxon
Highest level is domain
All of life belongs to one of 3 domains
Bacteria, Archaea, and Eukarya

6. Land plants and relatives Alveolata Stramenopila Rhizaria Amoebozoa
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Domains:
Bacteria
Archaea
Eukarya
Eukaryotic
supergroups:
Excavata
Land plants and relatives
Alveolata
Stramenopila
Rhizaria
Amoebozoa
Opisthokonta
Typical protists:
Large eukaryotic
kingdoms:
Plantae
Fungi
Animalia

8. Every Species Is Placed into a Taxonomic Hierarchy
EVOLUTIONARY CONNECTIONS
Every Species Is Placed into a Taxonomic Hierarchy
Domain > Supergroup > Kingdom > Phylum > Class > Order > Family > Genus > Species
The plural of phylum is phyla
The plural of genus is genera

9. Taxonomic group Gray wolf found in Number of species
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Taxonomic
group
Gray wolf
found in
Number of
species
Domain
Eukarya
~4 –10 million
Supergroup
Opisthokonta
>1 million
Kingdom
Animalia
>1 million
Phylum
Chordata
~50,000
Class
Mammalia
~5,000
Order
Carnivora
~270
Family
Canidae 34
Genus
Canis 7
Species
lupus 1

10. All species (past and present) are related by an evolutionary history
BIOLOGY PRINCIPLE
All species (past and present) are related by an evolutionary history
A goal of taxonomy is to relate the diversity of species according to their evolutionary relationships.

11. Binomial nomenclature
Genus name and species epithet
ex: Homo sapiens
Genus name always Capitalized
Species epithet never capitalized
Both names either italicized
Rules for naming established and regulated by international associations

12. Phylogenetic Trees
Phylogeny – evolutionary history of a species or group of species
To propose a phylogeny, biologists use the tools of systematics
Trees are usually based on morphological or genetic data

13. Phylogenetic tree Diagram that describes phylogeny
A hypothesis of evolutionary relationships among various species
Based on available information
New species can be formed by
Anagenesis – single species evolves into a different species
Cladogenesis – a species diverges into two or more species

15. Millions of years ago (mya)
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Species (43) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64
Present
Genus(species
43–44)
Family (species
41–44)
Order (species
41–48)
Time
500 million
Millions of years ago (mya)
Class (species
33–48)
Phylum (species 33–64)
Kingdom (species 1–64)
1 billion

16. Monophyletic group or clade
Group of species – a taxon – consisting of the most recent common ancestor and all of its ancestors
Smaller and more recent clades are nested within larger clades that have older common ancestors

17. Homology
Similarities among various species that occur because they are derived from a common ancestor
ex: Bat wing, human arm and cat front leg
Genes can also be homologous if they are derived from the same ancestral gene

18. Morphological analysis
First systematic studies focused on morphological features of extinct and modern species
Convergent evolution (traits arising independently due to adaptation to similar environments) can cause problems

20. Millions of years ago (mya)
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Hippidium and
other genera
Equus 5
Stylohipparion
Nannippus
Neohipparion
Pliohippus
Hipparion 10
Callippus
Sinohippus
Megahippus
Archaeohippus
Merychippus 20
Anchitherium
Hypohippus
Time
Millions of years ago (mya)
Parahippus
Miohippus
Mesohippus
An analysis of fossilized bones
provided the phylogenetic tree
described here. 40
Paleotherium
Epihippus
Propalaeotherium
Pachynolophus
Orohippus 55
Hyracotherium

21. Structure determines function
BIOLOGY PRINCIPLE
Structure determines function
The changes in structural features during horse evolution are related to changes in their functional needs. During this time, horse populations shifted from feeding on leaves in forested regions to feeding on abrasive grasses in more wide-open spaces.
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22. Molecular systematics
Analysis of genetic data, such as DNA and amino acid sequences, to identify and study genetic homologies and propose phylogenetic trees
DNA and amino acid sequences from closely related species are more similar to each other than to sequences from more distantly related species

23. Cladistics
Study and classification of species based on evolutionary relationships
Cladistic approach discriminates among possible trees by considering the various possible pathways of changes and then choosing the tree that requires the least complicated explanation
Make phylogenetic trees or cladograms

24. Shared primitive character
Cladistic approach compares homologous traits, also called characters, which may exist in two or more character states
Shared primitive character
Shared by two or more different taxa and inherited from ancestors older than their last common ancestor
Shared derived character
Shared by two or more species or taxa and has originated in their most recent common ancestor
Basis of the cladistic approach is to analyze many shared derived characters to deduce the pathway that gave rise to those species

26. Branch point – two species differ in shared derived characters
Ingroup – group we are interested in
Outgroup – species or group of species that is assumed to have diverged before the species in the ingroup
An outgroup will lack one or more shared derived characters that are found in the ingroup

27. (a) Characteristics among species
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Lancelet
Lamprey
Salmon
Lizard
Rabbit
Mammary
glands
Tetrapod
Lancelet
Lamprey
Salmon
Lizard
Rabbit
Notochord
Yes
Yes
Yes
Yes
Yes
Hinged jaw
Vertebrae No
Yes
Yes
Yes
Yes
Hinged jaw No No
Yes
Yes
Yes
Tetrapod No No No
Yes
Yes
Vertebrae
Mammary
glands No No No No
Yes
Notochord
(a) Characteristics among species
(b) Cladogram based on morphological traits

28. Cladogram can also be constructed with gene sequences
7 species called A-G
A mutation that changes the DNA sequence is analogous to a change of a characteristic

29. GGTATAACCC GGTATTACCC GGTAGTACCC GGTAGTACCA GATAGTACCC GATAGTTCCC
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GGTATAACCC
GGTATTACCC
GGTAGTACCC
GGTAGTACCA
GATAGTACCC
GATAGTTCCC
GATA GTTCCG E D G F A B C
C10 G A7 T
C10 A G2 A T5 G A6 T
GGTATAACCC
Proposed primitive
sequence

30. Constructing a cladogram
Choose species
Choose characters
Determine polarity of character states
Primitive or derived?

31. Analyze cladogram
All species (or higher taxa) are placed on tips in the phylogenetic tree, not at branch points
Each cladogram branch point should have a list of one or more shared derived characters that are common to all species above the branch point unless the character is later modified
All shared derived characters appear together only once in a cladogram unless they arose independently during evolution more than once

32. Choose the most likely cladogram among possible options
Choose a noncontroversial outgroup as root

33. Principle of parsimony
Preferred hypothesis is the one that is the simplest for all the characters and their states
Challenge in a cladistic approach is to determine the correct polarity of events
It may not always be obvious which traits are primitive (came earlier) and which are derived (came later in evolution)
Fossils may be analyzed to help resolve

34. Example 4 taxa (A-D) A is the outgroup 3 potential trees
Has all primitive states
3 potential trees
Tree 3 requires fewest number of mutations so is the most parsimonous

35. According to the principle of parsimony, tree number 3 is the
more likely choice because it requires only five mutations.

36. Molecular Clocks
Favorable mutations are rare, detrimental mutations are quickly eliminated – so most mutations are neutral
If neutral mutations occur at a constant rate they can be used to measure evolutionary time
Not perfectly linear over long periods of time
Not all organisms evolve at the same rate
Differences in generation times

38. example: Primate evolution
Evolutionary relationships derived from DNA sequences for cytochrome oxidase subunit II
Tends to change fairly rapidly on an evolutionary timescale, so good for close relationships
Three branch points to examine (A, D, E)
Ancestor A
This ancestor diverged into two species that ultimately gave rise to siamangs and the other five species
23 million years for siamang genome to accumulate changes different from other 5 species

39. (Hylobates syndactylus)
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Common chimpanzees
(Pan troglodytes)
Pygmy chimpanzees
(Pan paniscus)
(Bonobos)
Present
Short time
(Gorilla gorilla)
Gorillas
(Homo sapiens)
Humans
(Pongo pygmaeus)
Orangutans
Moderate time
(Hylobates syndactylus)
Siamangs E 5 D 10 C
Long time to accumulate random neutral changes
Millions of years ago (mya)
Time 15 B 20 A 25

40. Ancestor D
This ancestor diverged into two species that eventually gave rise to humans and chimpanzees
Differences in gene sequences between humans and chimpanzees are relatively moderate
Ancestor E
This ancestor diverged into two species of chimpanzees
Two modern species of chimpanzees have fewer differences in their gene sequences

41. (Hylobates syndactylus)
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Common chimpanzees
(Pan troglodytes)
Pygmy chimpanzees
(Pan paniscus)
(Bonobos)
Present
Short time
(Gorilla gorilla)
Gorillas
(Homo sapiens)
Humans
(Pongo pygmaeus)
Orangutans
Moderate time
(Hylobates syndactylus)
Siamangs E 5 D 10 C
Long time to accumulate random neutral changes
Millions of years ago (mya)
Time 15 B 20 A 25

42. Horizontal Gene Transfer
Any process in which an organism incorporates genetic material from another organism without being the offspring of that organism
The transfer of genes between different species
In contrast to vertical evolution
The traditional view of evolution
Changes in groups due to descent from a common ancestor

43. Tree of Life – really a “Web of Life”
Horizontal gene transfer plays a significant role in the phylogeny of all living species
Still prevalent among prokaryotes but less common in eukaryotes
Horizontal gene transfer may have been so prevalent that the universal ancestor may have been a community of cell lineages

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