Chapter 21
Genomes and Their Evolution
Overview: Reading the Leaves from the Tree of Life
Complete genome sequences exist for a human, chimpanzee, E. coli, brewer’s yeast, nematode, fruit fly, house mouse, rhesus macaque, and other organisms
Comparisons of genomes among organisms provide information about the evolutionary history of genes and taxonomic groups
Genomics is the study of whole sets of genes and their interactions
Bioinformatics is the application of computational methods to the storage and analysis of biological data
Fig. 21-1
Concept 21.1: New approaches have accelerated the pace of genome sequencing
The most ambitious mapping project to date has been the sequencing of the human genome
Officially begun as the Human Genome Project in 1990, the sequencing was largely completed by 2003
The project had three stages:
Genetic (or linkage) mapping
Physical mapping
DNA sequencing
Three-Stage Approach to Genome Sequencing
A linkage map (genetic map) maps the location of several thousand genetic markers on each chromosome
A genetic marker is a gene or other identifiable DNA sequence
Recombination frequencies are used to determine the order and relative distances between genetic markers
Fig. 21-2-1
Cytogenetic map
Genes located
by FISH
Chromosome
bands
Fig. 21-2-2
Cytogenetic map
Genes located
by FISH
Chromosome
bands
Linkage mapping
1
Genetic
markers
Fig. 21-2-3
Cytogenetic map
Genes located
by FISH
Chromosome
bands
Linkage mapping
1
2
Genetic
markers
Physical mapping
Overlapping
fragments
Fig. 21-2-4
Cytogenetic map
Genes located
by FISH
Chromosome
bands
Linkage mapping
1
2
3
Genetic
markers
Physical mapping
Overlapping
fragments
DNA sequencing
A physical map expresses the distance between genetic markers, usually as the number of base pairs along the DNA
It is constructed by cutting a DNA molecule into many short fragments and arranging them in order by identifying overlaps
Sequencing machines are used to determine the complete nucleotide sequence of each chromosome
A complete haploid set of human chromosomes consists of 3.2 billion base pairs
Whole-Genome Shotgun Approach to Genome Sequencing
The whole-genome shotgun approach was developed by J. Craig Venter in 1992
This approach skips genetic and physical mapping and sequences random DNA fragments directly
Powerful computer programs are used to order fragments into a continuous sequence
Fig. 21-3-1
Cut the DNA
into overlapping
fragments short enough
for sequencing
1
2
Clone the fragments
in plasmid or phage
vectors.
Fig. 21-3-2
Cut the DNA
into overlapping
fragments short enough
for sequencing
1
2
3
Clone the fragments
in plasmid or phage
vectors.
Sequence each
fragment.
Fig. 21-3-3
Cut the DNA
into overlapping
fragments short enough
for sequencing
1
2
3
4
Clone the fragments
in plasmid or phage
vectors.
Sequence each
fragment.
Order the
sequences into
one overall
sequence
with computer
software.
Both the three-stage process and the whole-genome shotgun approach were used for the Human Genome Project and for genome sequencing of other organisms
At first many scientists were skeptical about the whole-genome shotgun approach, but it is now widely used as the sequencing method of choice
A hybrid of the two approaches may be the most useful in the long run
Concept 21.2 Scientists use bioinformatics to analyze genomes and their functions
The Human Genome Project established databases and refined analytical software to make data available on the Internet
This has accelerated progress in DNA sequence analysis
Centralized Resources for Analyzing Genome Sequences
Bioinformatics resources are provided by a number of sources:
National Library of Medicine and the National Institutes of Health (NIH) created the National Center for Biotechnology Information (NCBI)
European Molecular Biology Laboratory
DNA Data Bank of Japan
Genbank, the NCBI database of sequences, doubles its data approximately every 18 months
Software is available that allows online visitors to search Genbank for matches to:
A specific DNA sequence
A predicted protein sequence
Common stretches of amino acids in a protein
The NCBI website also provides 3-D views of all protein structures that have been determined
Fig. 21-4
Identifying Protein-Coding Genes Within DNA Sequences
Computer analysis of genome sequences helps identify sequences likely to encode proteins
Comparison of sequences of “new” genes with those of known genes in other species may help identify new genes
Understanding Genes and Their Products at the Systems Level
Proteomics is the systematic study of all proteins encoded by a genome
Proteins, not genes, carry out most of the activities of the cell
How Systems Are Studied: An Example
A systems biology approach can be applied to define gene circuits and protein interaction networks
Researchers working on Drosophila used powerful computers and software to predict 4,700 protein products that participated in 4,000 interactions
The systems biology approach is possible because of advances in bioinformatics
Fig. 21-5
Proteins
Application of Systems Biology to Medicine
A systems biology approach has several medical applications:
The Cancer Genome Atlas project is currently monitoring 2,000 genes in cancer cells for changes due to mutations and rearrangements
Treatment of cancers and other diseases can be individually tailored following analysis of gene expression patterns in a patient
In future, DNA sequencing may highlight diseases to which an individual is predisposed
Fig. 21-6
Concept 21.3 Genomes vary in size, number of genes, and gene density
By summer 2007, genomes had been sequenced for 500 bacteria, 45 archaea, and 65 eukaryotes including vertebrates, invertebrates, and plants
Genome Size
Genomes of most bacteria and archaea range from 1 to 6 million base pairs (Mb); genomes of eukaryotes are usually larger
Most plants and animals have genomes greater than 100 Mb; humans have 3,200 Mb
Within each domain there is no systematic relationship between genome size and phenotype
Table 21-1
Number of Genes
Free-living bacteria and archaea have 1,500 to 7,500 genes
Unicellular fungi have from about 5,000 genes and multicellular eukaryotes from 40,000 genes
Number of genes is not correlated to genome size
For example, it is estimated that the nematode
C. elegans has 100 Mb and 20,000 genes, while humans have 3,200 Mb and 20,488 genes
Vertebrate genomes can produce more than one polypeptide per gene because of alternative splicing of RNA transcripts
Gene Density and Noncoding DNA
Humans and other mammals have the lowest gene density, or number of genes, in a given length of DNA
Multicellular eukaryotes have many introns within genes and noncoding DNA between genes
Concept 21.4: Multicellular eukaryotes have much noncoding DNA and many multigene families
The bulk of most eukaryotic genomes consists of noncoding DNA sequences, often described in the past as “junk DNA”
Much evidence indicates that noncoding DNA plays important roles in the cell
For example, genomes of humans, rats, and mice show high sequence conservation for about 500 noncoding regions
Sequencing of the human genome reveals that 98.5% does not code for proteins, rRNAs, or tRNAs
About 24% of the human genome codes for introns and gene-related regulatory sequences
Intergenic DNA is noncoding DNA found between genes
Pseudogenes are former genes that have accumulated mutations and are nonfunctional
Repetitive DNA is present in multiple copies in the genome
About three-fourths of repetitive DNA is made up of transposable elements and sequences related to them
Fig. 21-7
Exons (regions of genes coding for protein
or giving rise to rRNA or tRNA) (1.5%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Introns and
regulatory
sequences
(24%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(15%)
L1
sequences
(17%)
Alu elements
(10%)
Simple sequence
DNA (3%)
Large-segment
duplications (5–6%)
Transposable Elements and Related Sequences
The first evidence for wandering DNA segments came from geneticist Barbara McClintock’s breeding experiments with Indian corn
McClintock identified changes in the color of corn kernels that made sense only by postulating that some genetic elements move from other genome locations into the genes for kernel color
These transposable elements move from one site to another in a cell’s DNA; they are present in both prokaryotes and eukaryotes
Fig. 21-8
Fig. 21-8a
Fig. 21-8b
Movement of Transposons and Retrotransposons
Eukaryotic transposable elements are of two types:
Transposons, which move within a genome by means of a DNA intermediate
Retrotransposons, which move by means of an RNA intermediate
Fig. 21-9
Transposon
New copy of
transposon
Insertion
Transposon
is copied
Mobile transposon
DNA of
genome
(a) Transposon movement (“copy-and-paste” mechanism)
Retrotransposon
New copy of
retrotransposon
Insertion
Reverse
transcriptase
RNA
(b) Retrotransposon movement
Fig. 21-9a
Transposon
New copy of
transposon
DNA of
genome
Transposon
is copied
Insertion
Mobile transposon
(a) Transposon movement (“copy-and-paste” mechanism)
Fig. 21-9b
Retrotransposon
New copy of
retrotransposon
Reverse
transcriptase
Insertion
RNA
(b) Retrotransposon movement
Sequences Related to Transposable Elements
Multiple copies of transposable elements and related sequences are scattered throughout the eukaryotic genome
In primates, a large portion of transposable element–related DNA consists of a family of similar sequences called Alu elements
Many Alu elements are transcribed into RNA molecules; however, their function is unknown
The human genome also contains many sequences of a type of retrotransposon called LINE-1 (L1)
L1 sequences have a low rate of transposition and may help regulate gene expression
Other Repetitive DNA, Including Simple Sequence DNA
About 15% of the human genome consists of duplication of long sequences of DNA from one location to another
In contrast, simple sequence DNA contains many copies of tandemly repeated short sequences
A series of repeating units of 2 to 5 nucleotides is called a short tandem repeat (STR)
The repeat number for STRs can vary among sites (within a genome) or individuals
Simple sequence DNA is common in centromeres and telomeres, where it probably plays structural roles in the chromosome
Genes and Multigene Families
Many eukaryotic genes are present in one copy per haploid set of chromosomes
The rest of the genome occurs in multigene families, collections of identical or very similar genes
Some multigene families consist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA products
Fig. 21-10
DNA
RNA transcripts
Nontranscribed
spacer
Transcription unit
18S
28S
5.8S
28S
5.8S
rRNA
18S
DNA
(a) Part of the ribosomal RNA gene family
Heme
Hemoglobin
-Globin
-Globin
-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11


2
1
2
1


G
A



Adult
Fetus
Embryo
Fetus
and adult
Embryo
(b) The human -globin and -globin gene families
Fig. 21-10a
(a) Part of the ribosomal RNA gene family
18S
28S
28S
18S
5.8S
5.8S
rRNA
DNA
DNA
RNA transcripts
Nontranscribed
spacer
Transcription unit
The classic examples of multigene families of nonidentical genes are two related families of genes that encode globins
α-globins and β-globins are polypeptides of hemoglobin and are coded by genes on different human chromosomes
Fig. 21-10b
(b) The human -globin and -globin gene families
Heme
Hemoglobin
-Globin
-Globin
-Globin gene family
-Globin gene family
Chromosome 16
Chromosome 11
2
1


2
1


G
A



Embryo
Embryo
Fetus
Fetus
and adult
Adult
Concept 21.5: Duplication, rearrangement, and mutation 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
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
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 7 mammalian species paints a hypothetical chromosomal evolutionary history
Fig. 21-11
Human chromosome 16
Blocks of DNA
sequence
Blocks of similar sequences in four mouse chromosomes:
7
8
16
17
The rate of duplications and inversions seems to have accelerated about 100 million years ago
This coincides with when large dinosaurs went extinct and mammals diversified
Chromosomal rearrangements are thought to contribute to the generation of new species
Some of the recombination “hot spots” associated with chromosomal rearrangement are also locations that are associated with diseases
Duplication and Divergence of Gene-Sized Regions of DNA
Unequal crossing over during prophase I of meiosis can result in one chromosome with a deletion and another with a duplication of a particular region
Transposable elements can provide sites for crossover between nonsister chromatids
Fig. 21-12
Transposable
element
Gene
Nonsister
chromatids
Crossover
Incorrect pairing
of two homologs
during meiosis
and
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
Fig. 21-13
Ancestral globin gene
Duplication of
ancestral gene
Mutation in
both copies
Transposition to
different chromosomes
Further duplications
and mutations
-Globin gene family
on chromosome 16
-Globin gene family
on chromosome 11
Evolutionary time



2
1







2
1




G
A


Subsequent duplications of these genes and random mutations gave rise to the present globin genes, which code for oxygen-binding proteins
The similarity in the amino acid sequences of the various globin proteins supports this model of gene duplication and mutation
Table 21-2
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 α-lactalbumin gene 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
Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling
The duplication or repositioning of exons has contributed to genome evolution
Errors in meiosis can result in an exon being duplicated on one chromosome and deleted from the homologous chromosome
In exon shuffling, errors in meiotic recombination lead to some mixing and matching of exons, either within a gene or between two nonallelic genes
Fig. 21-14
Epidermal growth
factor gene with multiple
EGF exons (green)
Fibronectin gene with multiple
“finger” exons (orange)
Exon
shuffling
Exon
shuffling
Exon
duplication
Plasminogen gene with a
“kringle” exon (blue)
Portions of ancestral genes
TPA gene as it exists today
How Transposable Elements Contribute to Genome Evolution
Multiple copies of similar transposable elements may facilitate recombination, or crossing over, between different chromosomes
Insertion of transposable elements within a protein-coding sequence may block protein production
Insertion of transposable elements within a regulatory sequence may increase or decrease protein production
Transposable elements may carry a gene or groups of genes to a new location
Transposable elements may also create new sites for alternative splicing in an RNA transcript
In all cases, changes are usually detrimental but may on occasion prove advantageous to an organism
Concept 21.6: Comparing genome sequences provides clues to evolution and development
Genome sequencing has advanced rapidly in the last 20 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
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
Fig. 21-15
Most recent
common
ancestor
of all living
things
Billions of years ago
4
3
2
1
0
Bacteria
Eukarya
Archaea
Chimpanzee
Human
Mouse
0
10
20
30
40
50
60
70
Millions of years ago
Comparing Distantly Related Species
Highly conserved genes are genes that have changed very little over time
These inform us about relationships among species that diverged from each other a long time ago
Bacteria, archaea, and eukaryotes diverged from each other between 2 and 4 billion years ago
Highly conserved genes can be studied in one model organism, and the results applied to other organisms
Comparing Closely Related Species
Genetic differences between closely related species can be correlated with phenotypic differences
For example, genetic comparison of several mammals with nonmammals helps identify what it takes to make a mammal
Human and chimpanzee genomes differ by 1.2%, at single base-pairs, and by 2.7% because of insertions and deletions
Several genes are evolving faster in humans than chimpanzees
These include genes involved in defense against malaria and tuberculosis, regulation of brain size, and genes that code for transcription factors
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
Fig. 21-16
Wild type: two normal
copies of FOXP2
EXPERIMENT
RESULTS
Heterozygote: one copy
of FOXP2 disrupted
Homozygote: both copies
of FOXP2 disrupted
Experiment 1: Researchers cut thin sections of brain and stained
them with reagents, allowing visualization of brain anatomy in a
UV fluorescence microscope.
Experiment 2: Researchers sepa-
rated each newborn pup from its
mother and recorded the number
of ultrasonic whistles produced by
the pup.
Experiment 1
Experiment 2
Wild type
Heterozygote
Homozygote
Number of whistles
Wild
type
Hetero-
zygote
Homo-
zygote
(No
whistles)
0
100
200
300
400
Fig. 21-16a
EXPERIMENT
RESULTS
Wild type: two normal
copies of FOXP2
Heterozygote: one copy
of FOXP2 disrupted
Homozygote: both copies
of FOXP2 disrupted
Experiment 1: Researchers cut thin sections of brain and stained
them with reagents, allowing visualization of brain anatomy in a
UV fluorescence microscope.
Experiment 1
Wild type
Heterozygote
Homozygote
Fig. 21-16b
EXPERIMENT
RESULTS
Wild type: two normal
copies of FOXP2
Heterozygote: one copy
of FOXP2 disrupted
Homozygote: both copies
of FOXP2 disrupted
Experiment 2: Researchers separated each newborn pup
from its mother and recorded the number of ultrasonic
whistles produced by the pup.
Experiment 2
Number of whistles
(No
whistles)
Wild
type
Hetero-
zygote
Homo-
zygote
400
300
200
100
0
Comparing Genomes Within a Species
As a species, humans have only been around about 200,000 years and have low within-species genetic variation
Variation within humans is due to single nucleotide polymorphisms, inversions, deletions, and duplications
These variations are useful for studying human evolution and human health
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 major differences in form
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
Fig. 21-17
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly
chromosome
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
Fig. 21-17a
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly
chromosome
Fig. 21-17b
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
Related homeobox sequences have been found in regulatory genes of yeasts, plants, and even prokaryotes
In addition to homeotic genes, many other developmental genes are highly conserved from species to species
Fig. 21-18
Thorax
Genital
segments
Thorax
Abdomen
Abdomen
Sometimes small changes in regulatory sequences of certain genes lead to major changes in body form
For example, variation in Hox gene expression controls variation in leg-bearing segments of crustaceans and insects
In other cases, genes with conserved sequences play different roles in different species
Comparison of Animal and Plant Development
In both plants and animals, development relies on a cascade of transcriptional regulators turning genes on or off in a finely tuned series
Molecular evidence supports the separate evolution of developmental programs in plants and animals
Mads-box genes in plants are the regulatory equivalent of Hox genes in animals
Fig. 21-UN1
Bacteria
Archaea
Genome
size
Number
of genes
Gene
density
Most are 1–6 Mb
1,500–7,500
Higher than in eukaryotes
Introns
None in
protein-coding
genes
Other
noncoding
DNA
Very little
Present in
some genes
Can be large amounts;
generally more repetitive
noncoding DNA in
multicellular eukaryotes
Unicellular eukaryotes:
present, but prevalent only
in some species
Multicellular eukaryotes:
present in most genes
Lower than in prokaryotes
(Within eukaryotes, lower
density is correlated with
larger genomes.)
5,000–40,000
Most are 10–4,000 Mb, but
a few are much larger
Eukarya
Fig. 21-UN2
Fig. 21-UN3
You should now be able to:
Explain how linkage mapping, physical mapping, and DNA sequencing each contributed to the Human Genome Project
Define and compare the fields of proteomics and genomics
Describe the surprising findings of the Human Genome Project with respect to the size of the human genome
Distinguish between transposons and retrotransposons
Explain how polyploidy may facilitate gene evolution
Describe in general terms the events that may have led to evolution of the globin superfamily
Explain the significance of the rapid evolution of the FOXP2 gene in the human lineage
Provide evidence that suggests that the homeobox DNA sequence evolved very early in the history of life