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Genomes and Their Evolution: Biology
Genomes and Their Evolution: Biology
Genomes and Their Evolution: Biology
Biology
Eighth Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
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
Genes located
by FISH
Fig. 21-2-2
Cytogenetic map Chromosome
bands
Genes located
by FISH
1 Linkage mapping
Genetic
markers
Fig. 21-2-3
Cytogenetic map Chromosome
bands
Genes located
by FISH
1 Linkage mapping
Genetic
markers
2 Physical mapping
Overlapping
fragments
Fig. 21-2-4
Cytogenetic map Chromosome
bands
Genes located
by FISH
1 Linkage mapping
Genetic
markers
2 Physical mapping
Overlapping
fragments
3 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
3 Sequence each
fragment.
Fig. 21-3-3
1 Cut the DNA
into overlapping
fragments short enough
for sequencing
3 Sequence each
fragment.
4 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
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
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
Proteins
Application of Systems Biology to Medicine
Repetitive
DNA that Introns and
includes regulatory
transposable sequences
elements (24%)
and related
sequences
(44%)
Unique
noncoding
L1 DNA (15%)
sequences Repetitive
(17%) DNA
unrelated to
transposable
elements
(15%)
Alu elements
(10%)
Simple sequence Large-segment
DNA (3%) duplications (5–6%)
Transposable Elements and Related Sequences
DNA of
genome Transposon
is copied
Insertion
Mobile transposon
New copy of
Retrotransposon retrotransposon
RNA
Insertion
Reverse
transcriptase
New copy of
Transposon transposon
DNA of
genome Transposon
is copied
Insertion
Mobile transposon
New copy of
Retrotransposon retrotransposon
RNA
Insertion
Reverse
transcriptase
DNA
RNA transcripts Heme -Globin
Nontranscribed Hemoglobin
spacer Transcription unit
-Globin
5.8S
28S
Fetus
Embryo and adult Embryo Fetus Adult
18S
(a) Part of the ribosomal RNA gene family (b) The human -globin and -globin gene families
Fig. 21-10a
DNA
RNA transcripts
Nontranscribed
spacer Transcription unit
DNA
5.8S
28S
18S
Heme -Globin
Hemoglobin
-Globin
2 1 G
A
2 1
Fetus
Embryo and adult Embryo Fetus Adult
Blocks of DNA
sequence
Transposable Gene
element
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
Duplication of
ancestral gene
Mutation in
Evolutionary time
both copies
Transposition to
different chromosomes
Further duplications
and mutations
2 1
G A
2 1
Epidermal growth
factor gene with multiple
EGF exons (green) Exon Exon
shuffling duplication
Bacteria
Most recent
common
ancestor
Eukarya
of all living
things
Archaea
4 3 2 1 0
Billions of years ago
Chimpanzee
Human
Mouse
70 60 50 40 30 20 10 0
Millions of years ago
Comparing Distantly Related Species
EXPERIMENT
Wild type: two normal Heterozygote: one copy Homozygote: both copies
copies of FOXP2 of FOXP2 disrupted of FOXP2 disrupted
Experiment 1: Researchers cut thin sections of brain and stained Experiment 2: Researchers sepa-
them with reagents, allowing visualization of brain anatomy in a rated each newborn pup from its
UV fluorescence microscope. mother and recorded the number
of ultrasonic whistles produced by
the pup.
RESULTS
Experiment 1 Experiment 2
Number of whistles
400
300
200
100
(No
Wild type Heterozygote Homozygote whistles)
0
Wild Hetero- Homo-
type zygote zygote
Fig. 21-16a
EXPERIMENT
Wild type: two normal Heterozygote: one copy Homozygote: both copies
copies of FOXP2 of FOXP2 disrupted of FOXP2 disrupted
RESULTS
Experiment 1
EXPERIMENT
Wild type: two normal Heterozygote: one copy Homozygote: both copies
copies of FOXP2 of FOXP2 disrupted of FOXP2 disrupted
RESULTS
Experiment 2
Number of whistles
400
300
200
100
(No
whistles)
0
Wild Hetero- Homo-
type zygote zygote
Comparing Genomes Within a Species
Fly
chromosome
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
Fig. 21-17a
Adult
fruit fly
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
Genital
Thorax segments Abdomen
Thorax 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
Number
of genes 1,500–7,500 5,000–40,000