1. Studying genetic mechanisms of change can provide insight into large-scale evolutionary change
An organism’s genome is the full set of genes it contains.
In eukaryotes, most of the genes are found in the nucleus, but genes are also present in plastids and chloroplasts.
Genes are shuffled in every generation of sexually reproducing organisms via meiosis and fertilization.

2. Studies of genomic evolution look at the genome of an organism as an integrated whole and attempt to answer questions such as:
How do proteins acquire new functions?
Why are the genomes of different organisms so variable in size?
How has the enlargement of genomes been accomplished?

3. Concept 21.3 Genomes vary in size, number of genes, and gene density
By early 2010, over 1,200 genomes were completely sequenced, including 1,000 bacteria, 80 archaea, and 124 eukaryotes
Sequencing of over 5,500 genomes and over 200 metagenomes is currently in progress
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4. The Evolution of Genome Size
The size and composition of the genomes of many species show much variation.
Genome size varies greatly. Across broad taxonomic categories, there is some correlation between genome size and organism complexity.
Multicellular organisms have more DNA than single-celled organisms.
Generally, more complex organisms have more DNA than less complex organisms.

5. Table 21.1
Table 21.1 Genome Sizes and Estimated Numbers of Genes

6. Concept 21.4: Multicellular eukaryotes have much noncoding DNA and many multigene families
The bulk of most eukaryotic genomes neither encodes proteins nor functional RNAs
Much evidence indicates that noncoding DNA (previously called “junk DNA”) plays important roles in the cell
For example, genomes of humans, rats, and mice show high sequence conservation for about 500 noncoding regions
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7. The Evolution of Genome Size
If only the protein and RNA coding portions of genomes are considered (genes), there is much less variation in size.
Most of the variation in genome size is due to the amount of noncoding DNA an organism has.

8. Much of the noncoding DNA does not appear to have a function.
But it can alter the expression of surrounding genes.(regulatory genes)
Some noncoding DNA consists of pseudogenes (duplicated genes which are nonfunctional).
Some consists of transposable elements (repetetive DNA sequences that can move to different locations in the genome)

9. Regulatory sequences (20%)
Figure 21.7
Exons (1.5%)
Introns (5%)
Regulatory sequences (20%)
Repetitive DNA that includes transposable elements and related sequences (44%)
Unique noncoding DNA (15%)
L1 sequences (17%)
Figure 21.7 Types of DNA sequences in the human genome.
Repetitive DNA unrelated to transposable elements (14%)
Alu elements (10%)
Simple sequence DNA (3%)
Large-segment duplications (56%)

10. Concept 21.5: Mutations, Duplication, rearrangement of DNA contribute to genome evolution
The basis of change at the genomic level is mutation, which underlies much of genome evolution
The earliest forms of life likely had a minimal number of genes, including only those necessary for survival and reproduction
The size of genomes has increased over evolutionary time, with the extra genetic material providing raw material for gene diversification
© 2011 Pearson Education, Inc.

11. Mutation
Nucleic acids or genes evolve when nucleotide base substitutions occur.
Substitutions can change the amino acid sequence, and thus the structure and function, of the polypeptides.
By characterizing nucleic acid sequences and the primary structures of proteins, molecular evolutionists can determine how rapidly these macromolecules have changed and why they changed.

12. Nucleotide substitutions may or may not result in amino acid replacements.
Change in the amino acid sequence can change the charges, secondary and tertiary structure of a protein, and thus its function.

14. If an amino acid replacement does not make a difference with respect to fitness, the two rates are expected to be similar; the ratio would be close to one.
If an amino acid position is under strong stabilizing selection pressure, the rate of synonymous substitutions should be much higher than nonsynonymous.
If an amino acid position is under selection for change, the rate of nonsynonymous substitutions should be much higher than synonymous

16. The much slower rate of mutation at sites that do affect molecular function is consistent with the view that most nonsynonymous mutations are disadvantageous and are eliminated from the population by natural selection.
In general, the more essential a molecule is for cell function, the slower the rates of its evolution.

18. Comparing Genomes
Genome comparisons of closely related species help us understand recent evolutionary events
Genome comparisons of distantly related species help us understand ancient evolutionary events
Relationships among species can be represented by a tree-shaped diagram
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19. Most recent common ancestor of all living things
Figure 21.16
Bacteria
Most recent common ancestor of all living things
Eukarya
Archaea 4 3 2 1
Billions of years ago
Chimpanzee
Figure Evolutionary relationships of the three domains of life.
Human
Mouse 70 60 50 40 30 20 10
Millions of years ago

20. Concept 26.4: 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
DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
mtDNA evolves rapidly and can be used to explore recent evolutionary events

21. Comparison of DNA Sequences
Evolutionary changes are determined by comparing nucleotide or amino acid sequences among different organisms.
The longer two sequences have been evolving separately, the more differences they accumulate.
The timing of evolutionary changes can be determined and causes can be inferred.

22. Duplication of Entire Chromosome Sets
Accidents in meiosis can lead to one or more extra sets of chromosomes, a condition known as polyploidy
The genes in one or more of the extra sets can diverge by accumulating mutations; these variations may persist if the organism carrying them survives and reproduces
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23. Alterations of Chromosome Structure
Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs
Following the divergence of humans and chimpanzees from a common ancestor, two ancestral chromosomes fused in the human line
Duplications and inversions result from mistakes during meiotic recombination
Comparative analysis between chromosomes of humans and seven mammalian species paints a hypothetical chromosomal evolutionary history
© 2011 Pearson Education, Inc.

24. Chimpanzee chromosomes
Figure 21.12
Human chromosome 2
Chimpanzee chromosomes
Telomere sequences
Centromere sequences
Telomere-like sequences 12
Human chromosome 16
Mouse chromosomes
Centromere-like sequences
Figure Related chromosome sequences among mammals. 13 7 8 16 17
(a) Human and chimpanzee chromosomes
(b) Human and mouse chromosomes

25. Incorrect pairing of two homologs during meiosis
Figure 21.13
Nonsister chromatids
Gene
Transposable element
Crossover point
Incorrect pairing of two homologs during meiosis
Figure Gene duplication due to unequal crossing over.
and

26. Another way that genomes evolve is by gene duplications
Another way that genomes evolve is by gene duplications. Gene duplication may involve part of a gene, a single gene, parts of a chromosome, or whole chromosomes.
Copies may have one of four fates:
1.Both copies retain original function (more protein product could be made).
2. One copy accumulates substitutions that allow it to perform a new function
3. Both copies retain original or related function but expression diverges in different tissues or at different times.
4.One copy becomes nonfunctional from accumulation of deleterious substitutions and becomes a pseudogene.

27. Species C after many generations
Figure 26.18
(a)
Formation of orthologous genes:
a product of speciation
(b)
Formation of paralogous genes:
within a species
Ancestral gene
Ancestral gene
Ancestral species
Species C
Speciation with
divergence of gene
Gene duplication and divergence
Figure Two types of homologous genes
Orthologous genes
Paralogous genes
Species C after many generations
Species A
Species B

28. Evolution of Genes with Novel Functions
The copies of some duplicated genes have diverged so much in evolution that the functions of their encoded proteins are now very different
For example the lysozyme gene was duplicated and evolved into the gene that encodes α-lactalbumin in mammals
Lysozyme is an enzyme that helps protect animals against bacterial infection
α-lactalbumin is a nonenzymatic protein that plays a role in milk production in mammals
© 2011 Pearson Education, Inc.

29. Evolution of Genes with Related Functions: The Human Globin Genes
The genes encoding the various globin proteins evolved from one common ancestral globin gene, which duplicated and diverged about 450–500 million years ago
After the duplication events, differences between the genes in the globin family arose from the accumulation of mutations
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30. Table 21.2
Table 21.2 Percentage of Similarity in Amino Acid Sequence Between Human Globin Proteins

31. Duplication of ancestral gene
Figure 21.14
Ancestral globin gene
Duplication of ancestral gene
Mutation in both copies  
Transposition to different chromosomes
Evolutionary time  
Further duplications and mutations     
Figure A model for the evolution of the human -globin and -globin gene families from a single ancestral globin gene.     2 1   G A    2 1
-Globin gene family on chromosome 16
-Globin gene family on chromosome 11

32. Humans and chimpanzees differ in the expression of the FOXP2 gene, whose product turns on genes involved in vocalization
Differences in the FOXP2 gene may explain why humans but not chimpanzees communicate by speech
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33. Concept 21.6: Comparing genome sequences provides clues to evolution and development
Genome sequencing and data collection has advanced rapidly in the last 25 years
Comparative studies of genomes
Advance our understanding of the evolutionary history of life
Help explain how the evolution of development leads to morphological diversity
© 2011 Pearson Education, Inc.

34. Evolutionary Effects of Development Genes
Genes that program development control the rate, timing, and spatial pattern of changes in an organism’s form as it develops into an adult

35. Comparing Developmental Processes
Evolutionary developmental biology, or evo-devo, is the study of the evolution of developmental processes in multicellular organisms
Genomic information shows that minor differences in gene sequence or regulation can result in striking differences in form
© 2011 Pearson Education, Inc.

36. Changes in Spatial Pattern
Substantial evolutionary change can also result from alterations in genes that control the placement and organization of body parts
Homeotic genes determine such basic features as where wings and legs will develop on a bird or how a flower’s parts are arranged

37. Widespread Conservation of Developmental Genes Among Animals
Molecular analysis of the homeotic genes in Drosophila has shown that they all include a sequence called a homeobox
An identical or very similar nucleotide sequence has been discovered in the homeotic genes of both vertebrates and invertebrates
Homeobox genes code for a domain that allows a protein to bind to DNA and to function as a transcription regulator
Homeotic genes in animals are called Hox genes
© 2011 Pearson Education, Inc.

38. Fruit fly embryo (10 hours)
Figure 21.18
Adult fruit fly
Fruit fly embryo (10 hours)
Fly chromosome
Mouse chromosomes
Figure Conservation of homeotic genes in a fruit fly and a mouse.
Mouse embryo (12 days)
Adult mouse

39. Hox genes are a class of homeotic genes that provide positional information during development
If Hox genes are expressed in the wrong location, body parts can be produced in the wrong location
For example, in crustaceans, a swimming appendage can be produced instead of a feeding appendage

40. Evolution of vertebrates from invertebrate animals was associated with alterations in Hox genes
Two duplications of Hox genes have occurred in the vertebrate lineage
These duplications may have been important in the evolution of new vertebrate characteristics

41. Hypothetical vertebrate ancestor (invertebrate)
Fig
Hypothetical vertebrate
ancestor (invertebrate)
with a single Hox cluster
First Hox
duplication
Hypothetical early
vertebrates (jawless)
with two Hox clusters
Second Hox
duplication
Figure Hox mutations and the origin of vertebrates
Vertebrates (with jaws)
with four Hox clusters

42. Changes in Genes
New morphological forms likely come from gene duplication events that produce new developmental genes
A possible mechanism for the evolution of six-legged insects from a many-legged crustacean ancestor has been demonstrated in lab experiments
Specific changes in the Ubx gene have been identified that can “turn off” leg development

43. Hox gene 6 Hox gene 7 Hox gene 8 Ubx About 400 mya Drosophila Artemia
Fig
Hox gene 6
Hox gene 7
Hox gene 8
Ubx
About 400 mya
Figure Origin of the insect body plan
Drosophila
Artemia

44. Changes in Gene Regulation
Changes in the form of organisms may be caused more often by changes in the regulation of developmental genes instead of changes in their sequence
For example three-spine sticklebacks in lakes have fewer spines than their marine relatives
The gene sequence remains the same, but the regulation of gene expression is different in the two groups of fish

45. Concept 25.6: Evolution is not goal oriented
Evolution is like tinkering—it is a process in which new forms arise by the slight modification of existing forms

46. Changes in Rate and Timing
Heterochrony is an evolutionary change in the rate or timing of developmental events
It can have a significant impact on body shape
The contrasting shapes of human and chimpanzee skulls are the result of small changes in relative growth rates
Animation: Allometric Growth

47. Figure 25.19 Relative growth rates of body parts
Newborn 2 5 15
Adult
Age (years)
(a) Differential growth rates in a human
Figure Relative growth rates of body parts
Chimpanzee fetus
Chimpanzee adult
Human fetus
Human adult
(b) Comparison of chimpanzee and human skull growth

48. Heterochrony can alter the timing of reproductive development relative to the development of nonreproductive organs
In paedomorphosis, the rate of reproductive development accelerates compared with somatic development
The sexually mature species may retain body features that were juvenile structures in an ancestral species

49. Fig
Gills
Figure Paedomorphosis

50. Evolutionary Novelties
Most novel biological structures evolve in many stages from previously existing structures
Complex eyes have evolved from simple photosensitive cells independently many times
Exaptations are structures that evolve in one context but become co-opted for a different function
Natural selection can only improve a structure in the context of its current utility

51. (a) Patch of pigmented cells (b) Eyecup
Fig
Pigmented cells
(photoreceptors)
Pigmented
cells
Epithelium
Nerve fibers
Nerve fibers
(a) Patch of pigmented cells
(b) Eyecup
Fluid-filled cavity
Cellular
mass
(lens)
Cornea
Epithelium
Optic
nerve
Pigmented
layer (retina)
Optic nerve
(c) Pinhole camera-type eye
(d) Eye with primitive lens
Figure A range of eye complexity among molluscs
Cornea
Lens
Retina
Optic nerve
(e) Complex camera-type eye

52. Concept 26.5: Molecular clocks help track evolutionary time
To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

53. Neutral Theory
Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection
It states that the rate of molecular change in these genes and proteins should be regular like a clock
The neutral theory of molecular evolution:
The majority of mutations are neutral, and accumulate through genetic drift.
If a mutation confers an advantage, it quickly becomes fixed in a population.

54. Using the rationale that the rate of fixation of mutation is theoretically constant and equal to the neutral mutation rate, the concept of the molecular clock was developed.
The concept of the molecular clock states that macromolecules evolving in different populations should diverge from one another at a constant rate. The number of changes in these molecules can determine when the species diverged.
A molecule that illustrates this principle is the enzyme cytochrome c, a component of the respiratory chain in mitochondria.

55. Fig
Molecular clocks are calibrated against branches whose dates are known from the fossil record 90 60
Number of mutations 30
Figure A molecular clock for mammals 30 60 90
120
Divergence time (millions of years)

56. Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as neutral theory predicts
Irregularities result from natural selection in which some DNA changes are favored over others
Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty
The use of multiple genes may improve estimates

57. Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way
Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

58. Index of base changes between HIV sequences
Fig
0.20
0.15
Computer model
of HIV
Index of base changes between HIV sequences
0.10
Range
Figure Dating the origin of HIV-1 M with a molecular clock
0.05
1900
1920
1940
1960
1980
2000
Year