Transcript millions of years

CHAPTER 26
LECTURE
SLIDES
Prepared by
Brenda Leady
University of Toledo
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Taxonomy and systematics

Taxonomy
 Science
of describing, naming, and classifying
living and extinct organisms and viruses

Systematics
 Study
of biological diversity and the
evolutionary relationships among organisms,
both extinct and modern

Taxonomic groups are now based on
hypotheses regarding evolutionary
relationships derived from systematics
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Taxonomy
Hierarchical system involving successive
levels
 Each group at any level is called a taxon
 Domain

 Highest
level
 All of life belongs to one of 3 domains
 Bacteria, Archaea, and Eukarya
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Domains:
Eukaryotic
supergroups:
Large eukaryotic
kingdoms:
Bacteria
Excavata
Archaea
Eukarya
Land plants and algal relatives
Plantae
Alveolata
Stramenopila
Rhizaria
Amoebozoa
Opisthokonta
Fungi
Animalia
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Taxonomic
group
Gray wolf
found in
Number of
species
~ 4– 10 million
Domain
Eukarya
Supergroup
Opisthokonta
>1 million
Kingdom
Animalia
>1 million
Phylum
Chordata
~50,000
Class
Mammalia
~5,000
Order
Carnivora
~270
Family
Canidae
Genus
Canis
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Species
lupus
1
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Binomial nomenclature
Genus name and species epithet
 Genus name always capitalized
 Species epithet never capitalized
 Both names either italicized or underlined
 Rules for naming established and
regulated by international associations

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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

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Phylogenetic tree
Diagram that describes phylogeny
 A hypothesis of evolutionary relationships
among various species
 Based on available information
 New species can be formed by

– single species evolves into a
different species
 Cladogenesis – a species diverges into 2 or
more species
 Anagenesis
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Millions of years ago (mya)
Time
Present
F
I
G
J
B
5
H
K
E
C
D
B
10
A
9
10

Monophyletic group or clade
 Group
of species, 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
 Paraphyletic group

 Contains
a common ancestor and some, but
not all, of its descendents
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H
I
J
D
K
L
E
M
N
F
B
O
G
C
H
I
J
D
K
E
M
N
F
B
A
(a) Monophyletic
L
O
G
C
H
I
J
D
K
E
M
N
F
B
A
(b) Paraphyletic
L
O
G
C
A
(c) Polyphyletic
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KEY
Reptiles
(a) Reptiles as a
paraphyletic taxon
Birds
Crocodiles
Lizards
and snakes
Turtles
Birds
Crocodiles
Orders
Classes
Lizards
and snakes

Over time, taxonomic
groups will be
reorganized so only
monophyletic groups
are recognized
Reptiles were a
paraphyletic groups
because birds were
excluded
Turtles

Reptiles
(b) Reptiles as a
monophyletic taxon
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Homology
Similarities among various species that
occur because they are derived from a
common ancestor
 Bat wing, human arm and cat front leg
 Genes can also be homologous if they are
derived from the same ancestral gene

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Morphological analysis
First systematic studies focused on
morphological features of extinct and
modern species
 Convergent evolution (traits arise
independently due to adaptations to
similar environments) can cause problems

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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

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Cladistics



Study and classification of species based on
evolutionary relationships
Cladistic approach discriminates among
possible phylogenetic trees by considering the
various possible pathways of evolutionary
changes and then choosing the tree that
requires the least complex explanation for all of
the available data
Phylogenetic trees or cladograms
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

Cladistic approach compares homologous traits,
also called characters, which may exist in two or
more character states
Shared primitive character or symplesiomorphy
 Shared
by two or more different taxa and inherited
from ancestors older than their last common ancestor

Shared derived character or synapomorphy
 Shared
by two or more species or taxa and has
originated in their most recent common ancestor
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D
E
B
F
G
C
A
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Branch point – 2 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

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Notochord
Vertebrae
Hinged jaw
Tetrapod
Mammary
glands
Lancelet
Lamprey
Salmon
Lizard
Rabbit
Yes
No
No
No
No
Yes
Yes
No
No
No
Yes
Yes
Yes
No
No
Yes
Yes
Yes
Yes
No
Yes
Yes
Yes
Yes
Yes
(a) Characteristics among species
Lancelet
Lamprey
Salmon
Lizard
Rabbit
Mammary
glands
Tetrapod
Hinged jaw
Vertebrae
Notochord
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(b) Cladogram based on morphological traits



Cladogram can also
be constructed with
gene sequences
7 species called A-G
A mutation that
changes the DNA
sequence is
analogous to a
modification of a
characteristic
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Constructing a cladogram
1.
2.
3.
Choose species
Choose characters
Determine polarity of character states

Primitive or derived?
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4.
Analyze cladogram based on



5.
6.
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
Choose the most likely cladogram among
possible options
Choose a noncontroversial outgroup as root
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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
and came earlier and which are derived and came
later in evolution
 Fossils may be analyzed
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Example
4 taxa (A-D)
 A is the outgroup

 Has
all the primitive
states

3 potential trees
 Tree
3 requires
fewest number of
mutations so is the
most parsimonous
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According to the principle
of parsimony, tree
number 3 is the
more likely choice
because it requires only
five mutations.
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Molecular clocks





Favorable mutations rare and detrimental
mutations eliminated
Most mutations are neutral
If neutral mutations occur at a constant rate they
can be used to measure evolutionary time
Longer periods of time since divergence allows
for a greater accumulation of mutations
Not perfectly linear over long periods of time
 Not
all organisms evolve at the same rate
 Differences in generations times
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Nucleotide
differences in
a homologous
gene between
different pairs
of species
0
Evolutionary time since divergence of pairs of species
(millions of years)
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Primate evolution example

Evolutionary relationships derived by comparing
DNA sequences for cytochrome oxidase subunit
II
 Tends
to change fairly rapidly on an evolutionary
timescale


3 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
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
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
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Cooper and Colleagues Extracted DNA from Extinct
Flightless Birds and Modern Species to Propose a New
Phylogenetic Tree
Ancient DNA analysis or molecular
paleontology
 Under certain conditions DNA samples may
be stable as long as 50,000 – 100,000
years
 Discovery based sciences- gather data to
propose a hypothesis
 Sequences are very similar
 New Zealand colonized twice by the
ancestors of flightless birds

 First
by moa ancestor, then by kiwi ancestor
Horizontal gene transfer
Any process in which an organism
incorporates genetic material from another
organism without being the offspring of
that organism
 Vertical evolution

 Changes
in groups due to descent from a
common ancestor
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Due to Horizontal Gene Transfer, the
Tree of Life Is Really a “Web of Life”





Vertical evolution involves changes in species due
to descent from a common ancestor
Horizontal gene transfer is the transfer of genes
between different species
Significant role in 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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Bacteria
Archaea
Eukarya
Fungi
Animals
Plants
KEY
Vertical evolution
Horizontal gene transfer
Common ancestral community of primitive cells
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