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CAMPBELL BIOLOGY IN FOCUS
Urry • Cain • Wasserman • Minorsky • Jackson • Reece
18
Genomes and
Their Evolution
Lecture Presentations by
Kathleen Fitzpatrick and Nicole Tunbridge
© 2014 Pearson Education, Inc.
Overview: Reading the Leaves from the Tree
of Life
 Complete genome sequences exist for a human,
chimpanzee, E. coli and numerous other prokaryotes,
corn, fruit fly, house mouse, orangutan, and others
 Comparisons of genomes among organisms provide
information about the evolutionary history of genes
and taxonomic groups
© 2014 Pearson Education, Inc.
 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
© 2014 Pearson Education, Inc.
Figure 18.1
© 2014 Pearson Education, Inc.
Concept 18.1: The Human Genome Project
fostered development of faster, less expensive
sequencing techniques
 The Human Genome Project officially began in
1990, and the sequencing was largely completed
by 2003
 Even with automation, the sequencing of all 3 billion
base pairs in a haploid set presented a formidable
challenge
 A major thrust of the Human Genome Project was
the development of technology for faster sequencing
© 2014 Pearson Education, Inc.
Figure 18.2-1
1 Cut the DNA
into overlapping
fragments short
enough for
sequencing.
2 Clone the fragments
in plasmid or other
vectors.
© 2014 Pearson Education, Inc.
Figure 18.2-2
1 Cut the DNA
into overlapping
fragments short
enough for
sequencing.
2 Clone the fragments
in plasmid or other
vectors.
3 Sequence each
fragment.
© 2014 Pearson Education, Inc.
CGCCATCAGT
AGTCCGCTATACGA
ACGATACTGGT
Figure 18.2-3
1 Cut the DNA
into overlapping
fragments short
enough for
sequencing.
2 Clone the fragments
in plasmid or other
vectors.
3 Sequence each
fragment.
CGCCATCAGT
AGTCCGCTATACGA
CGCCATCAGT
ACGATACTGGT
ACGATACTGGT
4 Order the
sequences into one
overall sequence
with computer
software.
© 2014 Pearson Education, Inc.
AGTCCGCTATACGA
…CGCCATCAGTCCGCTATACGATACTGGT…
 The whole-genome shotgun approach was
developed by J. Craig Venter and colleagues
 This approach starts with cloning and sequencing
random DNA fragments
 Powerful computer programs are used to assemble
the resulting short overlapping sequences into a
single continuous sequence
© 2014 Pearson Education, Inc.
Concept 18.2: 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
 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
 BGI in Shenzhen, China
 This has accelerated progress in DNA sequence
analysis
© 2014 Pearson Education, Inc.
Identifying the Functions of Protein-Coding Genes
 DNA sequence may vary more than the protein
sequence does
 Scientists interested in proteins often compare the
predicted amino acid sequence of a protein with that
of other proteins
 Protein function can be deduced from sequence
similarity or a combination of biochemical and
functional studies
© 2014 Pearson Education, Inc.
Understanding Genes and Gene Expression at
the Systems Level
 Genomics is a rich source of insights into questions
about gene organization, regulation of expression,
growth and development, and evolution
 A project called ENCODE (Encyclopedia of DNA
Elements) has yielded a wealth of information about
protein-coding genes, genes for noncoding RNA,
and sequences that regulate DNA replication, gene
expression, and chromatin modification
© 2014 Pearson Education, Inc.
Systems Biology
 Proteomics is the systematic study of the full protein
sets (proteomes) encoded by genomes
 We must study when and where proteins are
produced in an organism in order to understand the
function of cells and organisms
 Systems biology aims to model the dynamic
behavior of whole biological systems based on the
study of interactions among the system’s parts
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Application of Systems Biology to Medicine
 A systems biology approach has several medical
applications
 The Cancer Genome Atlas project (completed in 2010)
attempted to identify all the common mutations in
three types of cancer by comparing gene sequences
and expression in cancer versus normal cells
 This was so fruitful that it will be extended to ten other
common cancers
 Silicon and glass “chips” have been produced that
hold a microarray of most known human genes
© 2014 Pearson Education, Inc.
Figure 18.4
© 2014 Pearson Education, Inc.
Concept 18.3: Genomes vary in size, number of
genes, and gene density
 By August of 2012, about 3,700 genomes had been
completely sequenced, including 3,300 bacterial,160
archaeal, and 183 eukaryotic genomes
 Sequencing of over 7,500 genomes and about 340
metagenomes was in progress
© 2014 Pearson Education, Inc.
Table 18.1
© 2014 Pearson Education, Inc.
Concept 18.4: Multicellular eukaryotes have much
noncoding DNA and many multigene families
 The bulk of most eukaryotic genomes encodes
neither proteins nor functional RNAs
 Sequencing of the human genome reveals that
98.5% does not code for proteins, rRNAs, or tRNAs
 About a quarter of the human genome codes for
introns and gene-related regulatory sequences
© 2014 Pearson Education, Inc.
 Intergenic DNA is noncoding DNA found between
genes
 Pseudogenes are former genes that have
accumulated mutations and are now 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
© 2014 Pearson Education, Inc.
Figure 18.5
Exons (1.5%)
L1
sequences
(17%)
Alu elements
(10%)
Regulatory
sequences (5%)
Introns
(20%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Unique
noncoding
DNA (15%)
Repetitive
DNA
unrelated to
transposable
elements
(14%)
Simple sequence DNA (3%)
© 2014 Pearson Education, Inc.
Large-segments
duplications (5–6%)
Transposable Elements and Related Sequences
 The first evidence for mobile 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 if 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
© 2014 Pearson Education, Inc.
Figure 18.6
© 2014 Pearson Education, Inc.
Movement of Transposons and Retrotransposons
 Eukaryotic transposable elements are of two types
 Transposons, which move by a “cut and paste”
method that sometimes leaves a copy behind
 Retrotransposons, which move by means of an
RNA intermediate and always leave a copy behind
© 2014 Pearson Education, Inc.
Figure 18.7
Transposon
DNA of
genome
Transposon
is copied
Mobile transposon
© 2014 Pearson Education, Inc.
New copy of
transposon
Insertion
Figure 18.8
Retrotransposon
New copy of
retrotransposon
Formation of a
single-stranded
RNA intermediate
RNA
Insertion
Reverse
transcriptase
© 2014 Pearson Education, Inc.
Sequences Related to Transposable Elements
 Multiple copies of transposable elements and related
sequences are scattered throughout eukaryotic
genomes
 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, if any, is
unknown
© 2014 Pearson Education, Inc.
 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
 STR diversity can be used to identify a unique set of
genetic markers for each individual, his or her
genetic profile
 Forensic scientists can use STR analysis on DNA
samples to identify victims of crime or natural
disasters
© 2014 Pearson Education, Inc.
Genes and Multigene Families
 Many eukaryotic genes are present in one copy per
haploid set of chromosomes
 The rest occur 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 rRNA products
© 2014 Pearson Education, Inc.
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
© 2014 Pearson Education, Inc.
Figure 18.10
Human
chromosome 2
Chimpanzee
chromosomes
Telomere
sequences
Centromere
sequences
Telomere-like
sequences
12
Centromere-like
sequences
13
© 2014 Pearson Education, Inc.
Figure 18.11
Large blocks of genes from human chromosome 16 can be
found on four mouse chromosomes
Human chromosome 16
Mouse chromosomes
7
8
Blocks of genes have stayed together during
evolution of mouse and human lineages
© 2014 Pearson Education, Inc.
16
17
Concept 18.6: Comparing genome sequences
provides clues to evolution and development
 Genome sequencing and data collection have
advanced rapidly in the last 25 years
 Comparative studies of genomes
 Reveal much about the evolutionary history of life
 Help clarify mechanisms that generated the great
diversity of present-day life-forms
© 2014 Pearson Education, Inc.
Figure 18.15
Bacteria
Most recent
common
ancestor
of all living
things
Eukarya
Archaea
4
3
2
Billions of years ago
1
0
Chimpanzee
Human
Mouse
70
60
50
40
30
20
Millions of years ago
© 2014 Pearson Education, Inc.
10
0
Comparing Distantly Related Species
 Highly conserved genes have remained similar over
time
 These help clarify relationships among species that
diverged from each other long ago
 Bacteria, archaea, and eukaryotes diverged from
each other between 2 and 4 billion years ago
 Comparative genomic studies confirm the relevance
of research on model organisms to our understanding
of biology in general and human biology in particular
© 2014 Pearson Education, Inc.
Comparing Genomes Within a Species
 As a species, humans have only been around about
200,000 years and have low within-species genetic
variation
 Most of the variation within humans is due to single
nucleotide polymorphisms (SNPs)
 There are also inversions, deletions, and duplications
and a large number of copy-number variants (CNVs)
 These variations are useful for studying human
evolution and human health
© 2014 Pearson Education, Inc.
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
 The vertebrate genes homologous to homeotic genes
of flies have kept the same chromosomal
arrangement
© 2014 Pearson Education, Inc.
Figure 18.17
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly
chromosome
Mouse
chromosomes
Mouse embryo
(12 days)
Adult mouse
© 2014 Pearson Education, Inc.
CAMPBELL BIOLOGY IN FOCUS
Urry • Cain • Wasserman • Minorsky • Jackson • Reece
22
Genomes and
Their Evolution
Lecture Presentations by
Kathleen Fitzpatrick and Nicole Tunbridge
© 2014 Pearson Education, Inc.
• Speciation is the process by which one species
splits into two or more species
• Speciation explains the features shared between
organisms due to inheritance from their recent
common ancestor
© 2014 Pearson Education, Inc.
• Speciation forms a conceptual bridge between
microevolution and macroevolution
• Microevolution consists of changes in allele
frequency in a population over time
• Macroevolution refers to broad patterns of
evolutionary change above the species level
© 2014 Pearson Education, Inc.
Concept 22.1: The biological species
concept emphasizes reproductive
isolation
• Species is a Latin word meaning “kind” or
“appearance”
• Biologists compare morphology, physiology,
biochemistry, and DNA sequences when
grouping organisms
© 2014 Pearson Education, Inc.
The Biological Species Concept
• The biological species concept states that a species
is a group of populations whose members have the
potential to interbreed in nature and produce viable,
fertile offspring; they do not breed successfully with
other populations
• Gene flow between populations holds the
populations together genetically
© 2014 Pearson Education, Inc.
Figure 22.2
(a) Similarity between different species
© 2014 Pearson Education, Inc.
(b) Diversity within a species
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
• Reproductive isolation can be classified by
whether barriers act before or after fertilization
© 2014 Pearson Education, Inc.
Figure 22.3
Prezygotic barriers
Habitat
isolation
Temporal
isolation
Behavioral
isolation
Mechanical
isolation
Postzygotic barriers
Gametic
isolation
MATING
ATTEMPT
(a)
(c)
(d)
(e)
(f)
Reduced
hybrid
viability
Reduced
Hybrid
hybrid
breakdown
fertility
VIABLE,
FERTILE
OFFSPRING
FERTILIZATION
(g)
(h)
(i)
(j)
(b)
(k)
© 2014 Pearson Education, Inc.
(l)
• 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
© 2014 Pearson Education, Inc.
Figure 22.3a
Prezygotic barriers
Habitat
isolation
Temporal
isolation
Behavioral
isolation
MATING
ATTEMPT
(a)
(c)
(d)
(b)
© 2014 Pearson Education, Inc.
(e)
Figure 22.3b
Prezygotic barriers
Mechanical
isolation
Gametic
isolation
MATING
ATTEMPT
(f)
© 2014 Pearson Education, Inc.
FERTILIZATION
(g)
Figure 22.3c
Postzygotic barriers
Reduced
hybrid
viability
Reduced Hybrid
hybrid breakdown
fertility
VIABLE,
FERTILE
OFFSPRING
FERTILIZATION
(h)
(i)
(j)
(k)
© 2014 Pearson Education, Inc.
(l)
Figure 22.3d
Prezygotic Habitat Temporal Behavioral
barriers
isolation isolation isolation
MATING
ATTEMPT
Mechanical Gametic
isolation isolation
MATING
ATTEMPT
Postzygotic
barriers
Reduced Reduced
Hybrid
hybrid
hybrid breakdown
viability fertility
FERTILIZATION
© 2014 Pearson Education, Inc.
FERTILIZATION
VIABLE,
FERTILE
OFFSPRING
Limitations of the Biological Species
Concept
• The biological species concept cannot be applied
to fossils or asexual organisms (including all
prokaryotes)
• The biological species concept emphasizes
absence of gene flow
• However, gene flow can occur between distinct
species
– For example, grizzly bears and polar bears can mate to
produce “grolar bears”
© 2014 Pearson Education, Inc.
Figure 22.4
Grizzly bear (U. arctos)
Hybrid “grolar bear”
Polar bear (U. maritimus)
© 2014 Pearson Education, Inc.
Other Definitions of Species
• Other species concepts emphasize the unity
within a species rather than the separateness of
different species
• The morphological species concept defines a
species by structural features
– It applies to sexual and asexual species but relies on
subjective criteria
© 2014 Pearson Education, Inc.
• The ecological species concept views a species in
terms of its ecological niche
– It applies to sexual and asexual species and emphasizes
the role of disruptive selection
• The phylogenetic species concept defines a
species as the smallest group of individuals on a
phylogenetic tree
– It applies to sexual and asexual species, but it can be
difficult to determine the degree of difference required
for separate species
© 2014 Pearson Education, Inc.
Concept 22.2: Speciation can take
place with or without geographic
separation
• Speciation can occur in two ways
– Allopatric speciation
– Sympatric speciation
© 2014 Pearson Education, Inc.
Figure 22.5
(a) Allopatric speciation: forms (b) Sympatric speciation: a subset
forms a new species without
a new species while
geographic separation.
geographically isolated.
© 2014 Pearson Education, Inc.
Evidence of Allopatric Speciation
• Fifteen pairs of sister species of snapping shrimp
(Alpheus) are separated by the Isthmus of Panama
• These species originated from 9 million to 3
million years ago, when the Isthmus of Panama
formed and separated the Atlantic and Pacific
waters
© 2014 Pearson Education, Inc.
Figure 22.7
A. formosus
A. nuttingi
ATLANTIC
OCEAN
Isthmus of Panama
PACIFIC
OCEAN
A. panamensis
© 2014 Pearson Education, Inc.
A. millsae
Figure 22.8
Experiment
Initial population
of fruit flies
(Drosophila
pseudoobscura)
Some flies raised
on starch medium
Some flies raised
on maltose medium
Mating experiments
after 40 generations
Results
22
9
8
20
Number of matings
in experimental group
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Starch
Starch
population 2 population 1
Maltose
Starch
Starch
population 1 population 2
Male
Starch
Starch
Female
Maltose
Male
Female
18
15
12
15
Number of matings
in control group
Sympatric (“Same Country”)
Speciation
• In sympatric speciation, speciation takes place in
populations that live in the same geographic area
• Sympatric speciation occurs when gene flow is
reduced between groups that remain in contact
through factors including
– Polyploidy
– Habitat differentiation
– Sexual selection
© 2014 Pearson Education, Inc.
Polyploidy
• Polyploidy is the presence of extra sets of
chromosomes due to accidents during cell division
• Polyploidy is much more common in plants than in
animals. Many important crops (oats, cotton,
potatoes, tobacco, and wheat) are polyploids
• An autopolyploid is an individual with more than
two chromosome sets, derived from one species
• The offspring of matings between autopolyploids
and diploids have reduced fertility
© 2014 Pearson Education, Inc.
Concept 22.3: Hybrid zones reveal
factors that cause reproductive
isolation
• A hybrid zone is a region in which members of
different species mate and produce hybrids
• Hybrids are the result of mating between species
with incomplete reproductive barriers
© 2014 Pearson Education, Inc.
Concept 22.4: Speciation can occur
rapidly or slowly and can result from
changes in few or many genes
• Many questions remain concerning how long it
takes for new species to form, or how many genes
need to differ between species
• Speciation can be studied using the fossil record,
morphological data, or molecular data
© 2014 Pearson Education, Inc.
Patterns in the Fossil Record
• The fossil record includes examples of species that
appear suddenly, persist essentially unchanged for
some time, and then apparently disappear
• These periods of apparent stasis punctuated by
sudden change are called punctuated equilibria
• The punctuated equilibrium model contrasts with a
model of gradual change in a species’ existence
© 2014 Pearson Education, Inc.
Figure 22.14
(a) Punctuated model
Time
(b) Gradual model
© 2014 Pearson Education, Inc.