1. Genomes and Their Evolution18
Genomes and Their Evolution

2. 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 2

3. 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 3

4. Figure 18.1
Figure 18.1 What genomic information distinguishes a human from a chimpanzee? 4

5. 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 5

6. Cut the DNA into overlapping fragments short enough for sequencing.
Figure 1
Cut the DNA
into overlapping
fragments short
enough for
sequencing. 2
Clone the fragments
in plasmid or other
vectors.
Figure Whole-genome shotgun approach to sequencing (step 1) 6

7. Cut the DNA into overlapping fragments short enough for sequencing.
Figure 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
ACGATACTGGT
Figure Whole-genome shotgun approach to sequencing (step 2) 7

8. …CGCCATCAGTCCGCTATACGATACTGGT…
Figure 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
ACGATACTGGT
Figure Whole-genome shotgun approach to sequencing (step 3)
CGCCATCAGT
ACGATACTGGT 4
Order the
sequences into one
overall sequence
with computer
software.
AGTCCGCTATACGA
…CGCCATCAGTCCGCTATACGATACTGGT… 8

9. This approach starts with cloning and sequencing random DNA fragments
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 9

10. 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 10

11. 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 11

12. 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 12

13. 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 13

14. 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 14

15. Figure 18.4
Figure 18.4 A human gene microarray chip 15

16. 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 16

17. Table 18.1
Table 18.1 Genome sizes and estimated numbers of genes 17

18. 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 18

19. 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 19

20. Simple sequence DNA (3%)
Figure 18.5
Exons (1.5%)
Regulatory
sequences (5%)
Introns
(20%)
Repetitive
DNA that
includes
transposable
elements
and related
sequences
(44%)
Unique
noncoding
DNA (15%) L1
sequences
(17%)
Figure 18.5 Types of DNA sequences in the human genome
Repetitive
DNA
unrelated to
transposable
elements
(14%)
Alu elements
(10%)
Large-segments
duplications (5–6%)
Simple sequence DNA (3%) 20

21. 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 21

22. Figure 18.6
Figure 18.6 The effect of transposable elements on corn kernel color 22

23. 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 23

24. New copy of transposon Transposon is copied
Figure 18.7
New copy of
transposon
Transposon
DNA of
genome
Transposon
is copied
Insertion
Figure 18.7 Transposon movement
Mobile transposon 24

25. New copy of retrotransposon Reverse transcriptase
Figure 18.8
New copy of
retrotransposon
Retrotransposon
Formation of a
single-stranded
RNA intermediate
RNA
Insertion
Reverse
transcriptase
Figure 18.8 Retrotransposon movement 25

26. 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 26

27. 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 27

28. 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 28

29. 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 29

30. 12 13 Human chromosome 2 Chimpanzee chromosomes Telomere sequences
Figure 18.10
Human
chromosome 2
Chimpanzee
chromosomes
Telomere
sequences
Centromere
sequences
Telomere-like
sequences 12
Centromere-like
sequences
Figure Related human and chimpanzee chromosomes 13 30

31. Figure 18.11
Large blocks of genes from human chromosome 16 can be found on four mouse chromosomes
Human chromosome 16
Mouse chromosomes
Figure A comparison of human and mouse chromosomes
Blocks of genes have stayed together during evolution of mouse and human lineages 31

32. 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 32

33. Bacteria Most recent common ancestor of all living things Eukarya
Figure 18.15
Bacteria
Most recent
common
ancestor
of all living
things
Eukarya
Archaea
Billions of years ago
Chimpanzee
Figure Evolutionary relationships of the three domains of life
Human
Mouse 30 20 10
Millions of years ago 33

34. 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 34

35. 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 35

36. 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 36

37. Adult fruit fly Fruit fly embryo (10 hours) Fly chromosome Mouse
Figure 18.17
Adult
fruit fly
Fruit fly embryo
(10 hours)
Fly
chromosome
Mouse
chromosomes
Figure Conservation of homeotic genes in a fruit fly and a mouse. Related homeobox sequences have been found in regulatory genes of yeasts and plants
The homeodomain is the part of the protein that binds to DNA when the protein functions as a transcriptional regulator
The more variable domains in the protein recognize particular DNA sequences and specify which genes are regulated by the protein
Mouse embryo
(12 days)
Adult mouse 37

38. Genomes and Their Evolution22
Genomes and Their Evolution

39. 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 39

40. 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 40

41. 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 41

42. 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 42

43. (a) Similarity between different species
Figure 22.2
Figure 22.2 The biological species concept is based on the potential to interbreed rather than on physical similarity
(a) Similarity between different species
(b) Diversity within a species 43

44. 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 44

45. Figure 22.3
Prezygotic barriers
Postzygotic barriers
Habitat
isolation
Temporal
isolation
Behavioral
isolation
Mechanical
isolation
Gametic
isolation
Reduced
hybrid
viability
Reduced
hybrid
fertility
Hybrid
breakdown
VIABLE,
FERTILE
OFF-
SPRING
MATING
ATTEMPT
FERTILI-
ZATION
(a)
(c)
(e)
(f)
(g)
(h)
(i)
(l)
(d)
(j)
(b)
Figure 22.3 Exploring reproductive barriers
(k) 45

46. 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 46

47. Habitat isolation Temporal isolation Behavioral isolation
Figure 22.3a
Prezygotic barriers
Habitat
isolation
Temporal
isolation
Behavioral
isolation
MATING
ATTEMPT
(a)
(c)
(e)
Figure 22.3a Exploring reproductive barriers (part 1: prezygotic barriers)
(d)
(b) 47

48. Mechanical isolation Gametic isolation
Figure 22.3b
Prezygotic barriers
Mechanical
isolation
Gametic
isolation
MATING
ATTEMPT
FERTILIZATION
(f)
(g)
Figure 22.3b Exploring reproductive barriers (part 2: prezygotic barriers) 48

49. Reduced hybrid viability Reduced hybrid fertility Hybrid breakdown
Figure 22.3c
Postzygotic barriers
Reduced
hybrid
viability
Reduced
hybrid
fertility
Hybrid
breakdown
VIABLE,
FERTILE
OFFSPRING
FERTILIZATION
(h)
(i)
(l)
(j)
Figure 22.3c Exploring reproductive barriers (part 3: postzygotic barriers)
(k) 49

50. Prezygotic barriers Habitat isolation Temporal isolation Behavioral
Figure 22.3d
Prezygotic
barriers
Habitat
isolation
Temporal
isolation
Behavioral
isolation
MATING
ATTEMPT
Mechanical
isolation
Gametic
isolation
MATING
ATTEMPT
FERTILIZATION
Figure 22.3d Exploring reproductive barriers (part 4: art summary)
Postzygotic
barriers
Reduced
hybrid
viability
Reduced
hybrid
fertility
Hybrid
breakdown
VIABLE,
FERTILE
OFFSPRING
FERTILIZATION 50

51. 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” 51

52. Grizzly bear (U. arctos) Polar bear (U. maritimus)
Figure 22.4
Grizzly bear (U. arctos)
Figure 22.4 Hybridization between two species of bears in the genus Ursus
Hybrid “grolar bear”
Polar bear (U. maritimus) 52

53. 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 53

54. 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 54

55. Concept 22.2: Speciation can take place with or without geographic separation
Speciation can occur in two ways
Allopatric speciation
Sympatric speciation 55

56. Allopatric speciation: forms a new species while
Figure 22.5
Figure 22.5 Two main modes of speciation
Allopatric speciation: forms
a new species while
geographically isolated.
(a)
(b)
Sympatric speciation: a subset
forms a new species without
geographic separation. 56

57. 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 57

58. A. formosus A. nuttingi ATLANTIC OCEAN Isthmus of Panama PACIFIC OCEAN
Figure 22.7
A. formosus
A. nuttingi
ATLANTIC
OCEAN
Isthmus of Panama
PACIFIC
OCEAN
Figure 22.7 Allopatric speciation in snapping shrimp (Alpheus)
A. panamensis
A. millsae 58

59. Initial population of fruit flies (Drosophila pseudoobscura)
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
Female
Female
Starch
population 1
Starch
population 2
Starch
Maltose
Figure 22.8 Inquiry: Can divergence of allopatric populations lead to reproductive isolation?
Starch
population 1
Starch 22 9 18 15
Male
Male
population 2
Starch
Maltose 8 20 12 15
Number of matings
in experimental group
Number of matings
in control group 59

60. 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 60

61. 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 61

62. 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 62

63. 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 63

64. 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 64

65. (a) Punctuated model Time (b) Gradual model Figure 22.14
Figure Two models for the tempo of speciation, based on patterns observed in the fossil record
(b) Gradual model 65