21 lecture genome and evolution

7/27/2019 21 Lecture Genome and Evolution

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LECTURE PRESENTATIONS

For CAMPBELL BIOLOGY, NINTH EDITIONJane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson

2011 Pearson Education, Inc.

Lectures by

Erin Barley

Kathleen Fitzpatrick

Genomes and Their Evolution

Chapter 21


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Overview: Reading the Leaves from the

Tree of Life Complete genome sequences exist for a human,

chimpanzee, E. coli, brewers yeast, corn, fruit fly,

house mouse, rhesus macaque, and otherorganisms

Comparisons of genomes among organisms

provide information about the evolutionary history

of genes and taxonomic groups



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Genomics is the study of whole sets of genesand their interactions

Bioinformatics is the application of

computational methods to the storage and

analysis of biological data



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Figure 21.1


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Concept 21.1: New approaches have

accelerated the pace of genome sequencing

The most ambitious mapping project to date hasbeen the sequencing of the human genome

Officially begun as the Human Genome Projectin 1990, the sequencing was largely completedby 2003

The project had three stages

Genetic (or linkage) mapping

Physical mapping

DNA sequencing



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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 distancesbetween genetic markers



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Figure 21.2-1

Cytogenetic map

Genes located

by FISH

Chromosome

bands


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Figure 21.2-2

Cytogenetic map

Genes located

by FISH

Chromosome

bands

Linkage mapping

Genetic

markers

1


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Figure 21.2-3

Cytogenetic map

Genes located

by FISH

Chromosome

bands

Linkage mapping

Genetic

markers

1

Physical mapping2

Overlapping

fragments


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Figure 21.2-4

Cytogenetic map

Genes located

by FISH

Chromosome

bands

Linkage mapping

Genetic

markers

1

Physical mapping2

Overlapping

fragments

DNA sequencing3


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A physical map expresses the distance betweengenetic 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



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Sequencing machines are used to determine thecomplete nucleotide sequence of each

chromosome

A complete haploid set of human chromosomes

consists of 3.2 billion base pairs



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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 mappingand sequences random DNA fragments directly

Powerful computer programs are used to order

fragments into a continuous sequence



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Cut the DNA intooverlapping frag-ments short enoughfor sequencing.

1

Clone the fragmentsin plasmid or phagevectors.

2

Figure 21.3-1


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1


2

Sequence eachfragment.

3

Figure 21.3-2


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1


2

Sequence eachfragment.

3

Order thesequences intoone overallsequencewith computer

software.

4

Figure 21.3-3


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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

The development of newer sequencingtechniques has resulted in massive increases in

speed and decreases in cost



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Technological advances have also facilitatedmetagenomics, in which DNA from a group of

species (a metagenome) is collected from an

environmental sample and sequenced

This technique has been used on microbial

communities, allowing the sequencing of DNA of

mixed populations, and eliminating the need to

culture species in the lab



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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



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Centralized Resources for Analyzing

Genome Sequences

Bioinformatics resources are provided by a

number of sources

National Library of Medicine and the NationalInstitutes of Health (NIH) created the National

Center for Biotechnology Information (NCBI)

European Molecular Biology Laboratory

DNA Data Bank of Japan BGI in Shenzhen, China



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Genbank, the NCBI database of sequences,doubles its data approximately every 18 months

Software is available that allows online visitors tosearch 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 allprotein structures that have been determined


Figure 21 4


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Figure 21.4


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Identifying Protein-Coding Genes and

Understanding Their Functions

Using available DNA sequences, geneticists can

study genes directly in an approach called reverse

genetics

The identification of protein coding genes within

DNA sequences in a database is called gene

annotation



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Gene annotation is largely an automated process Comparison of sequences of previously unknown

genes with those of known genes in other species

may help provide clues about their function



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Understanding Genes and Gene

Expression at the Systems Level

Proteomics is the systematic study of all proteins

encoded by a genome

Proteins, not genes, carry out most of theactivities of the cell



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How Systems Are Studied: An Example

A systems biology approach can be applied todefine gene circuits and protein interactionnetworks

Researchers working on the yeast

Saccharomyces cerevisiae used sophisticatedtechniques to disable pairs of genes one pair at atime, creating double mutants

Computer software then mapped genes to

produce a network-like functional mapof theirinteractions

The systems biology approach is possiblebecause of advances in bioinformatics


Figure 21 5


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Translation andribosomal functions

Nuclear-cytoplasmic

transport

RNA processing

Transcriptionand chromatin-

related functions

Mitochondrialfunctions

Nuclear migrationand proteindegradation

Mitosis

DNA replicationand repair

Cell polarity andmorphogenesis

Protein folding,glycosylation, and

cell wall biosynthesis

Secretionand vesicletransport

Metabolismand amino acid

biosynthesis

Peroxisomalfunctions

Glutamatebiosynthesis

Serine-related

biosynthesis

Amino acidpermease pathway

Vesiclefusion

Figure 21.5

Figure 21 5a


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Figure 21.5a

Translation andribosomal functions

Nuclear-

cytoplasmictransport

RNA processing

Transcriptionand chromatin-

related functions

Mitochondrialfunctions

Nuclear migrationand proteindegradation

Mitosis

DNA replicationand repair

Cell polarity andmorphogenesis

Protein folding,glycosylation, and

cell wall biosynthesis

Secretionand vesicletransport

Metabolism

and amino acidbiosynthesis

Peroxisomalfunctions

Figure 21.5b


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Glutamatebiosynthesis

Serine-

relatedbiosynthesis

Amino acidpermease pathway

Vesiclefusion

Metabolismand amino acid

biosynthesis

Figure 21.5b


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Application of Systems Biology to Medicine

A systems biology approach has several medicalapplications

The Cancer Genome Atlas project is currently

seeking all the common mutations in three types

of cancer by comparing gene sequences andexpression in cancer versus normal cells

This has been so fruitful, it will be extended to

ten other common cancers

Silicon and glass chipshave been produced

that hold a microarray of most known human

genes


Figure 21.6


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g


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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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Genome Size

Genomes of most bacteria and archaea rangefrom 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 3,000 Mb

Within each domain there is no systematic

relationship between genome size and phenotype


Table 21.1


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Number of Genes

Free-living bacteria and archaea have 1,500 to7,500 genes

Unicellular fungi have from about 5,000 genes

and multicellular eukaryotes up to at least 40,000

genes



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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

Drosophilahas 165 Mb and 13,700 genes

Vertebrate genomes can produce more than one

polypeptide per gene because of alternative

splicing of RNA transcripts



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Gene Density and Noncoding DNA

Humans and other mammals have the lowestgene density, or number of genes, in a given

length of DNA

Multicellular eukaryotes have many introns within

genes and noncoding DNA between genes



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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 importantroles in the cell

For example, genomes of humans, rats, and miceshow high sequence conservation for about 500noncoding regions



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Sequencing of the human genome reveals that98.5% does not code for proteins, rRNAs, ortRNAs

About a quarter of the human genome codes for

introns and gene-related regulatory sequences



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Intergenic DNA is noncoding DNA found betweengenes

Pseudogenes are former genes that haveaccumulated mutations and are nonfunctional

Repetitive DNAis present in multiple copies inthe genome

About three-fourths of repetitive DNA is made up

of transposable elements and sequences relatedto them


Figure 21.7Exons (1.5%) Introns (5%)


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Exons (1.5%) Introns (5%)

Regulatorysequences(20%)

UniquenoncodingDNA (15%)

RepetitiveDNAunrelated totransposableelements(14%)

Large-segment

duplications (56%)Simple sequence

DNA (3%)

A luelements(10%)

L1sequences(17%)

RepetitiveDNA thatincludestransposable

elementsand relatedsequences(44%)


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Transposable Elements and Related

Sequences

The first evidence for mobile DNA segmentscame from geneticist Barbara McClintocksbreeding experiments with Indian corn

McClintock identified changes in the color of cornkernels that made sense only by postulating thatsome genetic elements move from other genomelocations into the genes for kernel color

These transposable elements move from onesite to another in a cells DNA; they are present inboth prokaryotes and eukaryotes


Figure 21.8


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Figure 21.8a


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Figure 21.8b


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Movement of Transposons and

Retrotransposons Eukaryotic transposable elements are of two

types

Transposons, which move by means of a DNA

intermediate

Retrotransposons, which move by means of an

RNA intermediate


Figure 21.9


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Transposon

Transposonis copied

DNA of

genome

Mobile transposon

Insertion

New copy oftransposon

Figure 21.10


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Retrotransposon

New copy of

retrotransposon

Insertion

Reverse

transcriptase

RNA

Formation of a

single-stranded

RNA intermediate


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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

elementrelated DNA consists of a family of

similar sequences calledAlu elements

ManyAlu elements are transcribed into RNAmolecules; however their function, if any, is

unknown



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The human genome also contains manysequences of a type of retrotransposon called

LINE-1 (L1)

L1 sequences have a low rate of transposition

and may help regulate gene expression



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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



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A series of repeating units of 2 to 5 nucleotides iscalled 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



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Genes and Multigene Families

Many eukaryotic genes are present in one copyper haploid set of chromosomes

The rest of the genes 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


Figure 21.11


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DNARNA transcripts

Nontranscribed

spacer Transcription unit

DNA

18S 5.8S 28S

28S5.8S

18S

(a) Part of the ribosomal RNA gene family

-Globin

-Globin gene family

Chromosome 16

-Globin gene familyChromosome 11

-Globin

Heme

2

1 2 1 G A

(b) The human -globin and -globin gene familiesEmbryo

Fetus

and adult Fetus Adult

rRNA

Embryo

Figure 21.11a


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DNARNA transcripts

Nontranscribed


DNA

18S

5.8S

28S

28S

5.8S

18S

(a) Part of the ribosomal RNA gene family

rRNA

Figure 21.11c


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DNARNA transcripts

Nontranscribed



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The classic examples of multigene families ofnonidentical genes are two related families of

genes that encode globins

-globins and -globins are polypeptides of

hemoglobin and are coded by genes on differenthuman chromosomes and are expressed at

different times in development


Figure 21.11b


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-Globin

-Globin gene family

Chromosome 16


-Globin

Heme

2 1 2 1 G A

EmbryoFetus

and adult Fetus AdultEmbryo

(b) The human -globin and -globin gene families


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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 genomeevolution

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.


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Duplication of Entire Chromosome Sets

Accidents in meiosis can lead to one or moreextra sets of chromosomes, a condition known as

polyploidy

The genes in one or more of the extra sets can

diverge by accumulating mutations; thesevariations may persist if the organism carrying

them survives and reproduces



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Alterations of Chromosome Structure

Humans have 23 pairs of chromosomes, whilechimpanzees have 24 pairs

Following the divergence of humans andchimpanzees 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 ofhumans and seven mammalian species paints ahypothetical chromosomal evolutionary history


Figure 21.12


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Human

chromosome 2

Telomere

sequences

Centromere

sequences

Chimpanzee

chromosomes

12

Telomere-like

sequences

Centromere-like

sequences

Human

chromosome 16

13

(a) Human and chimpanzee chromosomes (b) Human and mouse chromosomes

7 8 16 17

Mouse

chromosomes

Figure 21.12aHuman

h 2

Chimpanzee

chromosomes


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chromosome 2

Telomere

sequences

Centromere

sequences

chromosomes

12

Telomere-like

sequences

Centromere-like

sequences

13

(a) Human and chimpanzee chromosomes

Figure 21.12b


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Human

chromosome 16

(b) Human and mouse chromosomes

7 8 16 17

Mouse

chromosomes


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The rate of duplications and inversions seems tohave accelerated about 100 million years ago

This coincides with when large dinosaurs wentextinct and mammals diversified

Chromosomal rearrangements are thought tocontribute to the generation of new species

Some of the recombination hot spotsassociatedwith chromosomal rearrangement are alsolocations that are associated with diseases



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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


Nonsister

chromatidsGene Transposable

element

Figure 21.13


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chromatids element

Crossover

point

and

Incorrect pairing

of two homologs

during meiosis


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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 450500

million years ago

After the duplication events, differences between

the genes in the globin family arose from the

accumulation of mutations


Figure 21.14


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Ancestral globin gene

-Globin gene family

on chromosome 16

-Globin gene familyon chromosome 11

Duplication of

ancestral gene

Mutation in

both copies

Transposition to

different chromosomes

Further duplications

and mutationsEvoluti

onarytime

2

12 1 G A


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Subsequent duplications of these genes andrandom 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 ofgene duplication and mutation


Table 21.2


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Evolution of Genes with Novel Functions

The copies of some duplicated genes havediverged so much in evolution that the functionsof their encoded proteins are now very different

For example the lysozyme gene was duplicated

and evolved into the gene that encodes-lactalbumin in mammals

Lysozyme is an enzyme that helps protectanimals against bacterial infection

-lactalbumin is a nonenzymatic protein thatplays a role in milk production in mammals



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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


Figure 21.15


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Exon

duplication

Exon

shuffling

Exonshuffling

F EGF K K

K

F F F F

EGF EGF EGF EGF

Epidermal growth

factor gene with multipleEGF exons

Fibronectin gene with multiple

fingerexons

Plasminogen gene with akringleexon

Portions of ancestral genes TPA gene as it exists today


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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 aregulatory sequence may increase or decrease

protein production



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Transposable elements may carry a gene orgroups of genes to a new position

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


C 21 6 C i


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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 developmentleads to morphological diversity


C i G


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Comparing Genomes

Genome comparisons of closely related specieshelp 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


Most recentBacteria

Figure 21.16


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Most recent

common

ancestor

of all living

things

Eukarya

Archaea

Chimpanzee

Human

Mouse

Millions of years ago

Billions of years ago

4 3 2

010203040506070

01

C i Di t tl R l t d S i


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Comparing Distantly Related Species

Highly conserved genes have changed very littleover time

These help clarify relationships among speciesthat diverged from each other long ago

Bacteria, archaea, and eukaryotes diverged fromeach other between 2 and 4 billion years ago

Highly conserved genes can be studied in onemodel organism, and the results applied to otherorganisms


C i Cl l R l t d S i


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Comparing Closely Related Species

Genetic differences between closely relatedspecies can be correlated with phenotypic

differences

For example, genetic comparison of several

mammals with nonmammals helps identify what ittakes to make a mammal



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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 and in regulation of

brain size, and genes that code for transcriptionfactors



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Humans and chimpanzees differ in the expressionof the FOXP2 gene, whose product turns on

genes involved in vocalization

Differences in the FOXP2 gene may explain why

humans but not chimpanzees communicate byspeech


Figure 21.17


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EXPERIMENT

Wild type: two normal

copies of FOXP2

RESULTS

Heterozygote: one

copy of FOXP2disrupted

Homozygote: both

copies of FOXP2disrupted

Experiment 1: Researchers cut thin sections of brain and stained

them with reagents that allow visualization of brain anatomy in a

UV fluorescence microscope.

Experiment 1 Experiment 2

Experiment 2: Researchers separated

each newborn pup from its mother

and recorded the number of

ultrasonic whistles produced by the

pup.

Wild type Heterozygote Homozygote

Numbero

fwhistles 400

300

200

100

0Wild

type

Hetero-

zygoteHomo-

zygote

(No

whistles)

EXPERIMENT

Figure 21.17a


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copies of FOXP2

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 that allow visualization of brain anatomy in a

UV fluorescence microscope.

Experiment 1

Wild type Heterozygote Homozygote

EXPERIMENTFigure 21.17b


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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

ofwhistles 400

300

200

100

0Wild

type

Hetero-

zygote

Homo-

zygote

(No

whistles)

RESULTS

Figure 21.17c


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Wild type

Figure 21.17d


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Heterozygote

Figure 21.17e


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Homozygote

Figure 21.17f


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Comparing GenomesWithin a Species


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Comparing Genomes Within a Species

As a species, humans have only been aroundabout 200,000 years and have low within-

species genetic variation

Variation within humans is due to single

nucleotide polymorphisms, inversions, deletions,and duplications

Most surprising is the large number of copy-

number variants

These variations are useful for studying human

evolution and human health


Comparing Developmental Processes


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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 instriking differences in form


Widespread Conservation of Developmental


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Widespread Conservation of Developmental

Genes Among Animals

Molecular analysis of the homeotic genes inDrosophilahas shown that they all include asequence called a homeobox

An identical or very similar nucleotide sequencehas been discovered in the homeotic genes ofboth vertebrates and invertebrates

Homeobox genes code for a domain that allows aprotein to bind to DNA and to function as atranscription regulator

Homeotic genes in animals are called Hox genes


Figure 21.18

Adult

fruit fly


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fruit fly

Fruit fly embryo(10 hours)

Fly chromosome

Mouse

chromosomes

Mouse embryo

(12 days)

Adult mouse

Figure 21.18a


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Adultfruit fly

Fruit fly embryo

(10 hours)

Fly chromosome

Figure 21.18b


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Mouse

chromosomes

Mouse embryo

(12 days)

Adult mouse


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Related homeobox sequences have been foundin regulatory genes of yeasts, plants, and even

prokaryotes

In addition to homeotic genes, many other

developmental genes are highly conserved fromspecies to species



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Sometimes small changes in regulatorysequences of certain genes lead to major

changes in body form

For example, variation in Hox gene expression

controls variation in leg-bearing segments ofcrustaceans and insects

In other cases, genes with conserved sequences

play different roles in different species


Figure 21.19

Thorax Abdomen

Genitalsegments


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Thorax Abdomen

Comparison of Animal and Plant


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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 regulatoryequivalent of Hox genes in animals


Archaea EukaryaBacteria

Figure 21.UN01


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Most are 16 MbGenomesize

Number ofgenes

Genedensity

Introns

OthernoncodingDNA Very little

None inprotein-codinggenes

Present insome genes

Higher than in eukaryotes

1,5007,500 5,00040,000

Most are 104,000 Mb, but afew are much larger

Lower than in prokaryotes(Within eukaryotes, lowerdensity is correlated with largergenomes.)

Unicellular eukaryotes:present, but prevalent only insome speciesMulticellular eukaryotes:

present in most genes

Can be large amounts;generally more repetitivenoncoding DNA inmulticellular eukaryotes

Protein-coding,RNA d

Human genomeFigure 21.UN02


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rRNA, andtRNA genes (1.5%)

Introns andregulatory

sequences (26%)

Repetitive DNA(green and teal)

Figure 21.UN03


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-Globin gene family

Chromosome 16


2

12 1 G A

Figure 21.UN04


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Figure 21.UN05


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Crossover

point

Figure 21.UN06


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21 lecture genome and evolution

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