Phylogeny is the evolutionary history of a species or group of related species
The discipline of systematics classifies organisms according to their phylogenies
Fossil, molecular, and genetic techniques are used to reconstruct evolutionary relationships, often using a âfamily treeâ approach
Is it the same as regular family tree of people?
2
Phylogeny and the Tree of Life
â¹#âº
2
3
From Darwinâs notebook on The Beagle: His handwriting is almost as bad as mine!
3
Binomial Nomenclature
Taxonomy is the ordered grouping (classification) and naming of organisms
In the 18th century, Carl âCarolusâ Linnaeus published a system of taxonomy based on resemblances
Two key features of his system remain useful today: two-part names for species and hierarchical classification
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4
The two-part scientific name of a species is called a binomial. The first part of the name is the genus
The second, called the specific epithet, is only unique for a species within each genus. This is usually descriptive in Latin or Greek, and is the only rank that is not a proper noun.
Thus, only both parts uniquely name the species, not the specific epithet alone.
The first letter of the genus is capitalized, and both parts are italicized when typing or underlined when writing, e.g., Homo sapiens (What is the translation?)
5
Hierarchical Classification
Linnaeus also introduced a system for grouping species in increasingly broad categories
The main taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
Did King Philip Come Over For Good Soup?
A taxonomic unit at any level of hierarchy is known as a taxon (plural = taxa)
â¹#âº
7
A phylogenetic tree represents a hypothesis about evolutionary relationships, which may or may not align with Linnaean taxonomy
Each node represents the divergence of a lineage into 2+ lineages, i.e., speciation (?)
Sister taxa are groups that share an immediate common ancestor. There can be ties in degree of relatedness.
A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
8
Linking Classification and Phylogeny
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8
Fig. 26-5
Sister
taxa
ANCESTRAL
LINEAGE
Taxon A
Polytomy
Common ancestor of
taxa AâF
Branch point
(node)
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
9
9
Sorting Homology from Analogy
Organisms with similar morphologies or DNA sequences are generally more closely related than those with different structures/sequences
However, we must distinguish whether a similarity is the result of homology or analogy
Homology is similarity due to shared ancestry, thus is the type properly used for constructing phylogenetic trees
10
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10
Humerus
Radius
Ulna
Carpals
Metacarpals
Phalanges
Human
Whale
Cat
Bat
Fig. 22-17
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11
Analogy is similarity NOT due to shared ancestry (convergent evolution, molecular and other coincidences)
Convergent evolution occurs when selection in similar environmental contexts produces similar features in different lineages
Such similarities obscure ancestry, thus should be omitted when constructing phylogenies
12
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12
13
Marsupial (above) and placental (below) moles separately evolved to burrow. Their similarities are therefore a mixture of analogies for digging and homologies inherited from the common ancestor of all mammals.
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Cladistics
Cladistics, the primary technique in use today, seeks to group organisms by common descent
A clade is a group of species that includes an ancestral species and all its descendants
Clades can be nested within larger clades, but must correspond to a separate and complete unit of ancestry
When using this approach, trees may be called cladograms (I just stick with âphylogenyâ)
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14
A valid clade is deemed monophyletic (one history): it incorporates all descendants of a common ancestor, that ancestor often being extinct or unknown.
15
Archosaurs
Bat
Crocodile
Stegosaurus
Hawk
Giraffe
Turtle
Tyrannosaurus
Velociraptor
â¹#âº
15
A paraphyletic grouping consists of an some, but not all, descendants. (?)The purple group plus turtles and crocodilians represents reptiles and is also paraphyletic. Thus, many argue for revision of bird-reptile taxonomy.
16
Dinosaurs
Bat
Crocodile
Stegosaurus
Hawk
Giraffe
Turtle
Tyrannosaurus
Velociraptor
â¹#âº
16
A polyphyletic group contains various taxa with different most recent ancestors. (?)The purple grouping is based on having wings, but they are analogous. Throw in winged insects and you have a legendary example of how NOT to make a .
17
Bat
Crocodile
Stegosaurus
Hawk
Giraffe
Turtle
Tyrannosaurus
Velociraptor
Flying Vertebrates
â¹#âº
17
Fig. 26-10
A
A
A
B
B
B
C
C
C
D
D
D
E
E
E
F
F
F
G
G
G
Group III
Group II
Group I
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group
18
âCladistsâ argue that taxonomy should be overhauled to be based on clades (i.e., discrete evolutionary units) rather than arbitrary similarities or convention. They used to be nasty but dialed it down once they beat out (or subsumed) the other approaches.
18
In comparison with an ancestor, each organism has both shared and different characteristics
A shared ancestral character is a trait that originated in an ancestor of the taxon
A shared derived character represents an evolutionary novelty unique to a clade
Like homology/analogy, a trait can be either ancestral or derived, depending on which groups are being compared
Inferring Phylogenies Using Derived Characters
19
Phylogenetic Trees as Hypotheses
The best hypothesis for a phylogenetic tree fits the most data: morphological, molecular, fossil
Phylogenetic bracketing exemplifies how trees can be used for further inquiry, sometimes allowing us to reconstruct features of an ancestor from its descendants
This has been applied to infer dinosaur nesting behavior from their closest living relatives, birds and crocodiles
21
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21
Eggs
Front limb
Hind limb
(a) Fossil remains of Oviraptor
and eggs
(b) Artistâs reconstruction of the dinosaurâs posture
22
Fossils of dinosaurs have been found on fossilized nests. Does this mean they brooded their eggs on the nest, or perhaps just coincidence? Phylogenies may be brought to bear on other research questions.
22
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Birds
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Saurischian
dinosaurs
23
Dinosaurs are bracketed by living groups that brood eggs in nests. This suggests that dinosaurs did as well, (?) otherwise brooding would have evolved or been lost multiple times. All else equal, this is less probable.
23
From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Five kingdoms were later recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
Recently, a three-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced genomes (esp. rRNA)
24
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24
Fig. 26-21
Fungi
EUKARYA
Trypanosomes
Green algae
Land plants
Red algae
Forams
Ciliates
Dinoflagellates
Diatoms
Animals
Amoebas
Cellular slime molds
Leishmania
Euglena
Green nonsulfur bacteria
Thermophiles
Halophiles
Methanobacterium
Sulfolobus
ARCHAEA
COMMON
ANCESTOR
OF ALL
LIFE
BACTERIA
(Plastids, including
chloroplasts)
Green
sulfur bacteria
(Mitochondrion)
Cyanobacteria
Chlamydia
Spirochetes
25
25
There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer is the movement of genes from one genome to another
Horizontal gene transfer complicates efforts to build a tree of life
26
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26
Fig. 26-22
3
Archaea
Bacteria
Eukarya
Billions of years ago
4
2
1
0
27
27
Because the earliest organisms exchanged substantial amounts of DNA, perhaps we should change the tree of life to the ring of life.
One ring to rule them allâ¦
28
I: Evolution
If I have seen further it is by standing on the shoulders of Giants.
— Sir Isaac Newton
1
Theories in Science
In the context of scientific inquiry, a theory is:
A conceptual framework supported by a large body of evidence
Broader in scope than a hypothesis. A theory ties information together and leads to specific testable hypotheses
In other words, a theory is a big deal in science, NOT a synonym for guessing
2
2
3
(This used to be a joke, but Iâm not laughing anymore.)
3
Historical Overview
What can explain both the unity and diversity of life on Earth?
Organic evolution: genetically based change over time. It acts on individuals in the present, but only manifests in the population over generations.
Natural Selection: mechanism causing the match between organisms and their environment (adaptive evolution = adaptation)
4
4
Traditional views involved unchanging and perfect species inhabiting a young Earth (Old Testament, Linnaeus, etc.)
The emergence of paleontology and geology helped lay the groundwork for Darwinâs contributions
Other areas of research also influenced his thinking, including studies on human population growth
6
6
Fig. 22-2
American Revolution
French Revolution
U.S. Civil War
1900
1850
1800
1750
1795
1809
1798
1830
1831â1836
1837
1859
1837
1844
1858
The Origin of Species is published.
Wallace sends his hypothesis to Darwin.
Darwin begins his notebooks.
Darwin writes essay on descent with modification.
Darwin travels around the world on HMS Beagle.
Malthus publishes âEssay on the Principle of Population.â
Lyell publishes Principles of Geology.
Lamarck publishes his hypothesis of evolution.
Hutton proposes his theory of gradualism.
Linnaeus (classification)
Cuvier (fossils, extinction)
Malthus (population limits)
Lamarck (species can change)
Hutton (gradual geologic change)
Lyell (modern geology)
Darwin (evolution, natural selection)
Wallace (evolution, natural selection)
7
7
Younger stratum
with more recent
fossils
Layers of deposited
sediment
Older stratum
with older fossils
8
8
Several 18th century naturalists (including Erasmus Darwin) suggested life evolves as environments change
Jean-Baptiste Lamarck hypothesized that species evolve through use and disuse of body parts and subsequent inheritance of acquired characteristics
This mechanism is unsupported by evidence (e.g., even if you and your mate lost the same finger, your children would still be born with all ten), but it did refocus subsequent research
Lamarckâs Hypothesis
9
9
10
The miniature phenotype of Bonsai trees is caused by manipulations of a bonsai master, not genetics. Would the next generation still be stunted if we planted their seeds and allowed them to grow naturally?
11
12
After first studying medicine, then theology at Cambridge, Darwin took an unpaid position as naturalist for a 5-year voyage around the world
During his travels on HMS Beagle, he collected thousands of specimens of plants and animals
He also observed and noted adaptations of plants and animals that inhabited diverse environments, including the renowned Galápagos finches.
Darwinâs Research
13
13
14
In 1844, Darwin wrote an essay on the origin of species and natural selection but did not introduce his theory publicly, anticipating an uproar
In 1858, Darwin received a manuscript from Alfred Russell Wallace, who had developed a theory of natural selection similar to Darwinâs
Darwin quickly finished The Origin of Species and published it the next year
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15
NORTH
AMERICA
EUROPE
AFRICA
AUSTRALIA
GREAT
BRITAIN
SOUTH
AMERICA
ATLANTIC
OCEAN
PACIFIC
OCEAN
Cape of
Good Hope
Tierra del Fuego
Cape Horn
Tasmania
New
Zealand
Andes
Equator
The
Galápagos
Islands
Pinta
Marchena
Genovesa
Santiago
Daphne
Islands
Pinzón
Fernandina
Isabela
San
Cristobal
Santa
Fe
Santa
Cruz
Florenza
Española
16
16
Darwin never used the word evolution in the first edition of The Origin of Species
The phrase descent with modification summarized Darwinâs perception of the unity and diversity of life: unity comes from common descent and diversity comes from subsequent modification
The history of life is like a tree with branches, where nodes represent common ancestors
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17
18
18
The Origin of Species (1859)
Darwin developed two main ideas in his book:
Descent with modification (i.e., evolution) explains the unity and diversity of life
Natural selection causes the match between organisms and their environment (adaptation)
He reviewed the evidence for the first, and started the second part by making some key observations, then drawing inferences:
19
19
Observation 1: Members of a population often vary greatly in their traits
Observation 2: Traits can be inherited from parents to offspring
Observation 3: All species are capable of producing more offspring than the environment can support
Observation 4: Owing to lack of food or other resources, many of these offspring do not survive
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20
Phenotypic variation in a single snail species
21
21
This is a photo of a puffball fungus expelling millions of spores as an example of great reproductive capacity.
Just one of these fungi could blanket the entire terrestrial surface of Earth with its offspring if environmental conditions did not prevent it.
22
22
Inference #1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals
Inference #2: This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations
23
23
(b) A stick mantid
in Africa
(a) A flower mantid
in Malaysia
24
24
If three conditions are met, natural selection WILL operate in a population:
Phenotypic variation must:
1. exist among individuals
2. be genetically heritable
3. affect reproductive success (fitness)
(variability, heritability, and fitness effects)
25
Pocket mice from the Tularosa Basin, NM
26
From Natural Selection to Speciation
Individuals with certain heritable characteristics survive and reproduce at a higher rate than other individuals
Natural selection increases the adaptation of organisms to their environment over time at the population level
If an environment changes over time, organisms move, or a barrier splits a population, then evolution by natural selection can generate new species (next lecture)
27
27
Evolution by natural selection is supported by an overwhelming amount of evidence. Note that each of these is an entire category that includes thousands of separate, peer reviewed studies:
Artificial Selection
The Fossil Record
Comparative Anatomy
Convergent Evolution
Molecular Data
Natural Populations
28
28
Artificial Selection
Darwin noted that humans have modified other species by selecting and breeding individuals with desired traits, a practice he dubbed artificial selection
Familiar examples include crop plants, livestock, and pets
29
29
For millennia, humans have selected certain ancestors to modify the traits of their descendants
30
31
31
The Fossil Record
The fossil record provides evidence of the extinction of species, the origin of new groups, and changes within groups over time
A Darwinian view of life predicts that evolutionary transitions should leave signs in the fossil record
Paleontologists have discovered fossils of many such transitional forms
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33
33
Trilobites evolving over millions of years at a single dig site
Trilobites and other fossils can be easily found in AZ, especially the Grand Canyon and Mogollon Rim areas.
https://www.npr.org/2020/08/21/904943006/fallen-boulder-reveals-313-million-year-old-fossil-footprints-at-grand-canyon
Bristolia insolens
Bristolia bristolensis
Bristolia harringtoni
Bristolia mohavensis
Latham Shale dig site, San
Bernardino County, California
Depth (meters)
0
2
4
6
8
10
12
14
16
18
1
2
3
3
1
2
4
4
34
34
35
These and many other âmissing linksâ have been found in the fossil record, just as evolutionary theory predicts.
35
35
The first fossil of Archaeopteryx was coincidentally discovered just as Darwin published his magnum opus, leading to accusations that his publishing co. fabricated it as a publicity stunt. Many more have been found around the world since then.
36
36
Comparative Anatomy
Homology is similarity resulting from common ancestry
Homologous structures are anatomical similarities that represent variations on a structural theme present in a common ancestor
37
37
Fig. 22-17
Humerus
Radius
Ulna
Carpals
Metacarpals
Phalanges
Human
Whale
Cat
Bat
38
38
Human embryo
Chick embryo
Pharyngeal
pouches
Post-anal
tail
Comparative embryology reveals anatomical homologies not visible in adult organisms (yep, we all had tails and gills before birth)
39
39
Vestigial structures, such as the pelvis âleftoversâ in marine mammals, still resemble ancestral structures but no longer have an apparent function.
40
40
Convergent Evolution (Analogy)
Convergent evolution is the development of similar, or analogous, features in distantly related groups
Analogous traits arise when groups independently adapt to similar environments in similar ways
Does not provide insight into ancestry (in fact, often obscures it), but does provide evidence of natural selection
41
41
Many placental mammals have a marsupial counterpart that evolved to fill the same niche âdown under.â
Because they did not come from a common ancestor, such convergences are analogous (seem the same), homologous not (are the same).
Sugar
glider
Flying
squirrel
AUSTRALIA
NORTH
AMERICA
42
42
Convergent body form among fast-swimming predators
43
43
An exploding body of molecular data supports the conclusion that evolution by natural selection has occurred and continues to do so.
More similar DNA sequences in closely related organisms, long-term genetic monitoring, selection on functional proteins, endosymbioses, etc.
Molecular Data
44
Thousands of studies have documented natural selection occurring in nature, including DDT resistance in mosquitos, antibiotic resistance in bacteria, and sexual selection in guppies
In addition to observations, countless manipulative experiments have shown natural selection occurring
Kettlewellâs studies of peppered moths provide a classic example of combining both approaches
Go to the following site, hit play, and become a virtual agent of natural selection! https://askabiologist.asu.edu/peppered-moths-game/
Natural Populations
45
PowerPoint® Lecture Presentations for Biology
Eighth Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp
Conditions on Early Earth
Chemical and physical processes on early Earth seem to have produced simple unicellular life. This was not spontaneous but over time through a sequence of stages:
1. Abiotic synthesis of small organic molecules
2. Joining of these into macromolecules
3. Packaging of molecules into membranes
4. Emergence of self-replicating molecules
2
See the following summary of how biology is a special subset of chemistry. Animations of the chemical reactions are particularly illustrative.
The Fossil Record
The fossil record reveals changes in the history of life on earth
Few individuals have fossilized, and even fewer have been discovered; the fossil record is incomplete and biased in favor of species:
That existed for a long time
Were abundant and widespread
Had hard parts capable of mineralizing
5
Dating rocks and fossils
Recall that sedimentary strata reveal the relative ages of fossils
The absolute ages of fossils can be determined by radiometric dating
A âparentâ isotope decays to a âdaughterâ isotope at a constant rate
Each isotope has a known half-life, the time required for half the parent isotope to decay
6
Radiocarbon dating can be used to date fossils up to 75,000 years old
For older fossils, some isotopes can be used to date sedimentary rock layers above and below the fossil
Reversals of the magnetic poles have left their signature on rocks throughout the world, also providing dating information
The geologic record is divided into the Archaean, the Proterozoic, and the Phanerozoic eons
The Phanerozoic encompasses multicellular eukaryotic life and is divided into 3 eras: the Paleozoic, Mesozoic, and Cenozoic (current)
Major boundaries correspond to extinction events in the fossil record
Focus on relative age and order. You need not memorize any numbers (or next 2 slides).
The History of Life
9
Fig 25-UN2
Prokaryotes
Billions of
years ago
4
3
2
1
12
12
The first single-celled organisms
The oldest known evidence of life are fossilized stromatolites, rock-like layers of bacteria and sediment
Stromatolites date back 3.5 billion years ago
Prokaryotes were the sole inhabitants of Earth until about 2.1 BYA
13
Fig 25-UN3
Atmospheric
oxygen
Billions of
years ago
4
3
2
1
15
15
The oxygen revolution
Most atmospheric oxygen is of biological origin, a byproduct of photosynthesis
By about 2.7 billion years ago, O2 began accumulating in the atmosphere and rusting iron-rich terrestrial rocks
The source was likely bacteria similar to modern cyanobacteria
16
17
Banded iron formations = evidence of oxygenic photosynthesis
Fig 25-UN4
Single-
celled
eukaryotes
Billions of
years ago
4
3
2
1
18
18
The first eukaryotes
The oldest fossils of eukaryotic cells date back 2.1 billion years
The theory of endosymbiosis explains that mitochondria and plastids (e.g., chloroplasts) were originally prokaryotes living within larger host cells
Ancestors of these organelles may have entered hosts as undigested prey or internal parasites
In the process of becoming more interdependent, they eventually became a single organism
19
20
Figure 25.9 A model of the origin of eukaryotes through serial endosymbiosis
Fig 25-UN5
Multicellular
eukaryotes
Billions of
years ago
4
3
2
1
21
21
The origin of multicellularity
The evolution of eukaryotic cells allowed for a greater range of unicellular forms, leading to emergence of colonial formsâ¦
A second wave of diversification occurred when true multicellularity evolved, giving rise to algae, plants, fungi, and animals
The oldest known multicellular fossils are small algae from about 1.2 BYA
22
Fig 25-UN7
Colonization of land
Billions of
years ago
4
3
2
1
23
23
The colonization of land
Multicellular organisms began to colonize land about 500 MYA
Plants and fungi likely colonized land together by 420 MYA
Arthropods and tetrapods then became the most widespread and diverse land animals
Would it even be possible for animals to establish themselves on land before plants and fungi? Our ecology section should provide insights on this.
Continental Drift
At three points, the land masses of Earth have formed a supercontinent
Earthâs continents move slowly over the underlying hot mantle
Oceanic and continental plates can collide, separate, or slide past each other
Interactions between plates cause earthquakes and formation of mountains and islands
25
Fig. 25-12b
(b) Major continental plates
Pacific
Plate
Nazca
Plate
Juan de Fuca
Plate
Cocos Plate
Caribbean
Plate
Arabian
Plate
African
Plate
Scotia Plate
North
American
Plate
South
American
Plate
Antarctic
Plate
Australian
Plate
Philippine
Plate
Indian
Plate
Eurasian Plate
27
27
Figure 25.12 Earth and its continental plates
Fig. 25-13a
South
America
Millions of years ago
65.5
Eurasia
India
Africa
Antarctica
Australia
North America
Madagascar
Cenozoic
Present
28
28
Figure 25.13 The history of continental drift during the Phanerozoic eon
Fig. 25-13b
Pangaea
Millions of years ago
135
Mesozoic
251
Paleozoic
Gondwana
Laurasia
29
29
Figure 25.13 The history of continental drift during the Phanerozoic eon
Formation of the supercontinent Pangaea about 250 MYA had many effects:
A reduction in shallow water and a colder, drier inland habitat
Changes in climate as continents moved toward and away from the poles
Changes in ocean circulation patterns leading to global cooling
The breakup of Pangaea likely caused widespread speciation (what kind?)
30
Mass Extinctions
The fossil record shows that most species that have ever lived are now extinct
At times, the rate of extinction has increased dramatically and caused a mass extinction
In each of the âbig fiveâ mass extinction events, more than 50% of Earthâs species became extinct
Evidence indicates that a sixth human-caused mass extinction is now occurring
31
Fig. 25-14
Total extinction rate
(families per million years):
Time (millions of years ago)
Number of families:
Cenozoic
Mesozoic
Paleozoic
E
O
S
D
C
P
Tr
J
542
0
488
444
416
359
299
251
200
145
Era
Period
5
C
P
N
65.5
0
0
200
100
300
400
500
600
700
800
15
10
20
32
32
Figure 25.14 Mass extinction and the diversity of life
Consequences of Mass Extinctions
Mass extinction can alter ecological communities and the niches available to organisms
It can take from 5 to 100 million years for diversity to recover following a mass extinction
Mass extinction can also pave the way for a process that is our next topic
33
Adaptive Radiation
Rapid speciation as individuals spread to new environments or evolve to carve new niches
Range from global to local, involving one or many ancestors
Largely understood at the microevolutionary level, and hypothesized to occur similarly at the macroevolutionary level
34
4. Colonization of islands.
5. Colonization of islands.
or
a.
b.
5. Species evolve different adap-
tations to minimize competition
with other species (character
displacement).
4. Species evolve different
adaptations in allopatry.
3. Populations on
different islands
evolve to become
different species.
2. The ancestral
species spreads
to different
islands.
1. An ancestral
species flies
from mainland
to colonize
one island.
35
Worldwide Adaptive Radiations
Mammals underwent radiation after the extinction of terrestrial dinosaurs
The Cambrian explosion saw the rapid emergence of most current animal phyla
Other notable radiations include photosynthetic prokaryotes, land plants, insects, and tetrapods
36
Fig. 25-17
Millions of years ago
Monotremes
(5 species)
250
150
100
200
50
ANCESTRAL
CYNODONT
0
Marsupials
(324 species)
Eutherians
(placental
mammals;
5,010 species)
Ancestral
mammal
37
37
Figure 25.17 Adaptive radiation of mammals
Regional Adaptive Radiations
Adaptive radiations can occur whenever organisms colonize new environments with little competition
The Hawaiian Islands are one of the worldâs great showcases of adaptive radiation
38
Fig. 25-18
Close North American relative,
the tarweed Carlquistia muirii
Argyroxiphium sandwicense
Dubautia linearis
Dubautia scabra
Dubautia waialealae
Dubautia laxa
HAWAII
0.4
million
years
OAHU
3.7
million
years
KAUAI
5.1
million
years
1.3
million
years
MOLOKAI
MAUI
LANAI
39
39
Figure 25.18 Adaptive radiation on the Hawaiian Islands
Evolutionary novelties
Most novel biological structures evolve in many stages from previous structures.
However, natural selection can only act in the context of its current utility. It must always pass the cost/benefit analysis to be favored (cannot build or save up for future generations).
Complex eyes have independently evolved from simple photosensitive cells at least two times: cephalopods and vertebrates.
40
41
Figure 25.24 A range of eye complexity among molluscs
Evolution is not goal oriented
Evolution is like tinkering: a process in which new forms arise by the modification of existing forms and structures.
Apparent trends should always be examined in a broad context, including both extinct and extant lineages.
Extracting a single evolutionary progression from the fossil record can be highly misleading.
E.g., things could have turned out very differently for the lineage leading to modern horses.
42
Origin of solar system
and Earth
4
3
2
1
Paleozoic
Meso-
zoic
Ceno-
zoic
Proterozoic
Archaean
Billions of
years ago
44
44
If the history of Earth were rescaled to an hour (minute hand on our âclockâ diagram),
humans would have originated less than
0.2 seconds ago!
45
Check out the following video that uses a football field to map key events in the history of life.
Recall that selection acts on individuals, but only populations evolve
Mutation and sexual reproduction produce the genetic variation that contributes to differences within a population (the âgene poolâ)
Variation in individual genotypes leads to variation in individual phenotypes
However, recall not all phenotypic variation is heritable (Why is this important?)
Population Genetics
2
Godfrey Hardy: English mathematician
Wilhelm Weinberg: German physician
concluded INDEPENDENTLY that:
1) In the absence of evolutionary pressure, allele and genotype frequencies (from 0 to 1) will remain constant across generations.
2) If mating is random, gene frequencies in the population relate to phenotypic frequencies by a simple mathematical formula. I.e., if you know one, you can calculate the other.
Hardy-Weinberg Equilibrium (1908)
3
Frequencies calculated using a binomial expansion:
(p+q)2 = p2 + 2pq + q2
p = frequency of first (e.g., dominant) allele
q = frequency of second (e.g., recessive) allele
p2 = individuals homozygous for first allele
2pq = individuals heterozygous for both alleles
q2 = individuals homozygous for second allele
The sum of allele frequencies will always be 1.0 (= 100%). Although the chapter keeps going, limit your study to the simplest case of two alleles.
4
Five forces can cause gene frequencies to change:
Mutation
Gene flow (migration)
Non-random mating
Genetic drift
Natural Selection
5
We can monitor phenotypes or genotypes to see if the equation predicts accurately across generations. Often it does not, and a population not in H-W equilibrium indicates that one or more of the 5 forces are operating. Thus, the population is evolving!
Mutagen
DNA
T
A
G
G
G
G
C
C
Self-fertilization
Mutation
Gene Flow
Nonrandom Mating
Genetic Drift
Selection
a. The ultimate source of
variation. Mutation
alone usually does not
alter overall allele
frequencies.
b. A very potent agent of
change. Individuals or
gametes move from one
population to another.
c. Inbreeding is the most
common form. Doesnât
always alter allele
frequency but changes
genotype frequency.
d. Statistical accidents.
The random fluctuation
in allele frequencies
increases as population
size decreases.
e. The only agent that
produces adaptive
evolutionary changes.
6
Natural Selection: A Closer Look
Natural selection is the only of the five forces that consistently results in adaptation
Selection brings about this match between organisms and their environment by acting on phenotypes, not genotypes. Nature cannot directly âseeâ genes inside an organism.
Relative fitness is a measure of the genetic contribution to subsequent generations compared to the most fit phenotype (usually set at 1.0)
Thus, nature indirectly favors, or selects, certain genotypes and their alleles based on relative fitness of their corresponding phenotypes
7
There are three modes of natural selection:
Directional selection favors individuals at one end of the phenotypic range
Disruptive selection favors individuals at both extremes of the phenotypic range
Stabilizing selection favors intermediate variants and acts against extremes of the phenotypic range
8
8
Fig. 23-13
Original population
(c) Stabilizing selection
(b) Disruptive selection
(a) Directional selection
Phenotypes (fur color)
Frequency of individuals
Original
population
Evolved
population
9
9
Figure 23.13 Modes of selection
Directional selection for negative phototropism in Drosophila lab experiment
10
Disruptive selection on beak size in black-bellied seedcracker finch in west Africa
11
Stabilizing selection for birth weight in humans
12
Why canât selection produce perfect organisms (e.g., why donât we have wheels)?
Selection can act only on existing variations
Evolution is limited by historical constraints
Adaptations are often compromises across multiple traits and environments
Chance, selection, and the environment interact so that maximum fitness is very much a moving target across space and time
13
In the Galápagos, Darwin discovered species of plants and animals found nowhere else on Earth.
Species is a Latin word meaning âkindâ or âappearanceâ
Biologists compare morphology, physiology, biochemistry, and molecular sequences when grouping organisms
Speciation, the process by which new species originate, is at the nexus of evolution
What is a species?
15
(a) Similarity between different species
(b) Diversity within a species
16
16
The Biological Species Concept
The BSC defines a species as a group whose members have the potential to interbreed in nature and produce viable, fertile offspring; they do not breed successfully with members of other species
It is used as a decision rule: Members of the same species? Yes or No
Because gene flow holds the phenotype of a population together, the BSC focuses on factors that restrict the flow of genetic material
17
Reproductive Isolation
Reproductive isolation is the existence of biological barriers that impede two species from producing viable, fertile offspring
Hybrids are the offspring of crosses between different species, thus apparently conflicting with our species definition (BSC)
To resolve this apparent conflict, biologists focused on the isolating mechanisms that keep closely related species separate despite overlapping ranges
18
Prezygotic barriers block fertilization from occurring by:
Impeding different species from attempting to mate
Preventing the successful completion of mating
Hindering fertilization if mating is successful
19
Habitat isolation: Two species do not encounter each other because they occupy different habitats, even though they are not isolated by physical barriers or geography.
Aquatic Thamnophis
Terrestrial Thamnophis
21
Temporal isolation: Species that breed at different times do not mix their gametes. Eastern spotted skunks breed only in spring while the western species breeds only in autumn. Their ranges overlap, but their breeding seasons do not.
Eastern spotted skunk
(Spilogale putorius)
Western spotted skunk
(Spilogale gracilis)
22
Behavioral isolation: Courtship rituals and other behaviors unique to a species can be effective barriers to reproduction. The dance of these blue footed boobies (think of clowns or fools, not breasts) allows them to identify potential mates of their own species. Like a passcode or secret handshake, mating will not proceed unless they get it right. (I usually do it in person, but instead see the video at the end of this PPT)
23
Mechanical isolation: Morphological differences can prevent successful mating. These two snail species have shells coiled in the opposite direction, causing their genitals to be on opposite sides when they try to copulate.
24
Gametic isolation: Sperm of one species may not be able to fertilize eggs of another species. Compatibility is checked by unique proteins of the gamete cell membranes.
25
Postzygotic barriers prevent the hybrid zygote from developing into a viable, fertile adult (hybrids have lower fitness than parental species, but not necessarily zero fitness):
Reduced hybrid viability
Reduced hybrid fertility
Hybrid breakdown
26
Reduced hybrid viability: Genes of the different parent species may interact to impair a hybridâs development. There is no healthy parent here for comparison, but this hybrid salamander is thin and slightly deformed.
28
Reduced hybrid fertility: Even if hybrids are vigorous, they may be sterile. E.g., mules, which are hybrids between horses and donkeys, represent an evolutionary dead end.
29
Hybrid breakdown: First-generation hybrids seem fine, but offspring of subsequent generations are feeble or sterile. Lower fitness of these rice plant hybrids (middle) takes 2 generations to reveal itself.
30
Other Definitions of Species
The biological species concept cannot be applied to fossils or asexual organisms including all prokaryotes
âPotential to interbreed in natureâ can be practically impossible to assess
Other species concepts emphasize unity within a species, rather than restricted gene flow between species
32
The morphological species concept defines a species by anatomical features
The ecological species concept emphasizes a speciesâ ecological niche (environmental role)
The phylogenetic species concept defines a species as the smallest group of individuals on a phylogenetic tree
They all usually agree on what is the same vs. separate species, but conflicts can arise.
Despite limitations, BSC is preferred for its objective criterion: ability to successfully reproduce. The other definitions are subjective.
33
Two Main Types of Speciation
Depending on whether or not groups are geographically separated when they diverge genetically:
Allopatric speciation
Sympatric speciation
34
Allopatric (âOther Countryâ) Speciation
Gene flow is interrupted or reduced when a species is divided into geographically isolated subpopulations
What constitutes a barrier depends on the ability of individuals to disperse. For example, not even the Grand Canyon will affect birds that routinely fly long distances (e.g., condors).
Separated populations will then evolve independently through mutation, natural selection, genetic drift, etc. They will diverge.
36
Sympatric (âSame Countryâ) Speciation
Sympatric speciation takes place in geographically overlapping populations
This can occur through several mechanisms, including:
– Polyploidy: chromosome issues (see text)
– Sexual Selection: non-random mating (see text and will come up again)
– Habitat Differentiation: e.g., insects living on different host plants
39
This fly species is in the process of speciation due to introduction of apple trees. Encounter rates and mating preferences are higher among individuals that grew up on the same kind of host fruit.
Hybrid zones provide opportunities to study speciation
A hybrid zone is a region in which members of different species mate and produce hybrids
Can occur in a single band or more complex patterns (e.g., a mosaic of parents and hybrids)
Hybrids often have reduced fitness compared with parent species, causing selection against hybridization
40
Fig. 24-13
EUROPE
Fire-bellied
toad range
Hybrid zone
Yellow-bellied
toad range
Yellow-bellied toad,
Bombina variegata
Fire-bellied toad,
Bombina bombina
Allele frequency (log scale)
Distance from hybrid zone center (km)
40
30
20
20
10
10
0
0.01
0.1
0.5
0.9
0.99
41
41
Hybrid Zones over Time (3 possible outcomes)
Reinforcement of reproductive barriers continues to split 2 species until no hybrids; should occur when hybrids are less fit than parents
Weakening of reproductive barriers leads to fusion back into 1 species (original or new?); should occur when hybrids are as fit, or more fit, than parents
Stability of the zone with continued formation of hybrids (3 groups, species status debatable); occurs when something prevents other outcomes
42
Speciation Rates and Genetics
(?) Hybrid zone studies indicate that much of our difficulty defining species comes from the fact that speciation is a process. We are sometimes asking for the outcome before it has been determined.
Questions remain concerning how long it takes for new species to form or how many genes need to differ between species
Broad patterns of speciation can be studied using the fossil record, morphological data, and molecular data
47
Patterns in the Fossil Record
There are many examples of species that appear suddenly, persist essentially unchanged for some time, and then disappear
Eldredge and Gould coined the term punctuated equilibrium to describe periods of apparent stasis punctuated by sudden change
This contrasts with gradualism, the traditional view of slow and steady changes over time
Debate has highlighted some interesting issues, but I would say the punctuated pattern is seen more often when looking across traits.
48
Fig. 24-17
(a) Punctuated pattern
(b) Gradual pattern
Time
49
49
Speciation Rates
Patterns in the fossil record and other studies suggest that speciation can be rapid or very slow
A large review shows the interval between speciation events ranges from about 4,000 years (some cichlids) to about 40,000,000 years. (some beetles), with a mean of 6.5 million years.
Note that speciation by polyploidy (very common among plants) can occur almost instantaneously. This type of sympatric speciation was not included in the analysis.
50
The Genetics of Speciation
The explosion of genomics has led to identification of specific genes involved in some cases of speciation
Speciation might require differences in a single, a few, or thousands of alleles
E.g., Japanese water snail: one gene change causes the shell to spiral in the opposite direction, leading to sympatric speciation by mechanical isolation
51
53
The dance of the blue footed booby is a classic example of behavioral isolation:
53
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