UNIT 20 EVOLUTIONARY GENETICS

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UNIT 20 EVOLUTIONARY GENETICS
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Explain the changes that occurred in the tree and
animal. Use your current understanding of
evolution by natural selection.
(AAAS 1999)
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Jean-Baptiste Lamarck (1744-1829) formulated new
ideas about the relationships between animals,
and then about the transmutation of species into
new ones.
Statue of Lamarck in the Jardin des Plantes,
Paris. The inscription reads, "Fondateur de la
doctrine de l'évolution" (Originator of the
doctrine of evolution)
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Lamarck developed two laws to explain evolution
the law of use and disuse, and the law of
inheritance of acquired characteristics. The
law of use and disuse In every animal which has
not passed the limit of its development, a more
frequent and continuous use of any organ
gradually strengthens, develops and enlarges that
organ, and gives it a power proportional to the
length of time it has been so used while the
permanent disuse of any organ imperceptibly
weakens and deteriorates it, and progressively
diminishes its functional capacity, until it
finally disappears.
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Lamarck developed two laws to explain evolution
the law of use and disuse, and the law of
inheritance of acquired characteristics. The
law of Inheritance of acquired characteristics
All the acquisitions or losses wrought by nature
on individuals, through the influence of the
environment in which their race has long been
placed, and hence through the influence of the
predominant use or permanent disuse of any organ
all these are preserved by reproduction to the
new individuals which arise, provided that the
acquired modifications are common to both sexes,
or at least to the individuals which produce the
young.
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Lamarck saw spontaneous generation as being
ongoing, with the simple organisms thus created
being transmuted over time (by his mechanism)
becoming more complex and closer to some notional
idea of perfection. As organisms became more
complex, they were replaced with new simple
organisms by the Creator.
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By the mid 1800s most scholars had abandoned the
view that species were immutable and had accepted
a view of change over time.
The question was how.
Darwins careful observations provided a natural
hypothesis as to how change could occur.
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• Darwins concept of evolution is based on three
  principles.
• The principle of variation Individuals in a
  population vary in traits
• The principle of heredity Traits can be passed
  from generation to generation
• The principle of survival Reproductive rates
  are too high to maintain population size and some
  individuals will die or fail to reproduce
  (selection)

For selection to be effective as an evolutionary
force, a trait must be heritable.
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Phyletic evolution continuous change over time
in a single line of descent Diversification
the origin of new species over time
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• SELECTION CAN ACT ON EXISTING VARIATION TO CHANGE
  ALLELE FREQUENCIES IN A POPULATION

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Darwins Finches
Phylogenetic tree A phylogenetic tree is a visual
representation in tree form of how we think
evolution has occurred.
Phylogenetic tree A phylogenetic tree is a visual
representation in tree form of how we think
evolution has occurred.
Darwins finches have been exhaustively studied
by the British team, Rosemary and Peter Grand
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Peppered Moths in Great Britain
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• SELECTION CAN ACT ON EXISTING VARIATION
• MULTIPLE ADAPTIVE PEAKS

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There is more than one outcome of selection.
Selection can alter a trait in a number of ways.
Selection increases fitness. Fitness can be
visualized as an adaptive landscape in which
there are high fitness peaks and low fitness
valleys.
Not all differences are adaptive some may be
due to chance events
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There is no single most adaptive
peak Organisms may increase fitness by
different routes The same adaptation may be
derived in different ways (homoplasy or
convergent evolution)
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The Antarctic ice fish
ANTIFREEZE PROTEINS Both Arctic and Antarctic
ice fish carry antifreeze proteins in their blood
but the genes that code for them differ in
sequence and arose millions of years apart. The
ice fish themselves could disappear as ocean
temperatures warm over the next century
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MULTIPLE ADAPTIVE PEAKS MALARIA PROTECTION IN
HETEROZYGOTES BETA HEMOGLOBIN S IN AFRICA BETA
HEMOGLOBIN C IN ASIA
C
S
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• THE PROCESS OF SPECIATION

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SPECIES CONCEPTS
Organisms are clustered into groups which share a
number of traits. We have no trouble knowing
distinguishing Drosophila melanogaster and D.
pseudoobscura and there are no hybrids between
these two species. They do not interbreed.
Not my type
Not my type
D. pseudoobscura
D. melanogaster
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SPECIES CONCEPTS
In other cases, species boundaries are not so
well defined or agreed upon. When do isolated
populations diverge sufficiently to be new
species?
Well ..........
Maybe?
D. pseudoobscura
D. melanogaster
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Marasmius androsaceus
Mating compatibility between M. androsaceus shows
two cryptic species
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• ALLOPATRIC SPECIATION
• Different geographical ranges

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Allopatric speciation speciation between
geographically separated populations. This is
the most common form of speciation.
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• SYMPATRIC SPECIATION
• Overlapping geographical ranges

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SYMPATRIC SPECIATION
Sympatric speciation, the formation of species in
the absence of geographical barriers, remains one
of the most contentious concepts in evolutionary
biology. Although speciation under sympatric
conditions seems theoretically possible,
empirical studies are scarce and only a few
credible examples of sympatric speciation exist.
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SYMPATRIC SPECIATION
A convincing case of sympatric speciation is
found in in the Midas cichlid species complex
(Amphilophus sp.) in a young and small volcanic
crater lake in Nicaragua. The study included
genetic markers (mitochondrial DNA,
microsatellites and amplified fragment length
polymorphisms), morphological and ecological
analyses.
Nature 439, 719-723 (9 February 2006)
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SYMPATRIC SPECIATION
Data suggest 1. Lake Apoyo was seeded only once
by the ancestral high-bodied bottom species
Amphilophus citrinellus, the most common cichlid
species in the area 2. A new elongated surface
species (Amphilophus zaliosus) evolved in Lake
Apoyo from the ancestral species (A. citrinellus)
in less than 10,000 yr 3. The two species in Lake
Apoyo are reproductively isolated 4. The two
species are eco-morphologically distinct
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Mimulus Two sympatric monkeyflower species that
are reproductively isolated owing to pollinator
preference by bumblebees or hummingbirds. Eight
floral traits were examined that determined
species differences.
For each trait we found at least one quantitative
trait locus accounting for more than 25 of the
phenotypic variance. This suggests that genes
of large effect can contribute to speciation
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POLYPLOIDY AND INSTANT SPECIATION
Polyploidy in plants creates instant species
and is a well-studied example of speciation
processes in plants.
Tetraploid X diploid ancestor
AABB X AA
AB
A
gametes
progeny
AAB
unbalanced genotype meiosis produces sterile
gametes
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• THE ORIGINS OF NEW GENETIC MATERIAL

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• Sources of new DNA
• Polyploidy/aneuploidy
• DNA duplications
• Transposable elements, retroviruses
• Horizontal transfers of DNA

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• THE ORIGINS OF NEW GENETIC MATERIAL
• Polyploidy/Aneuploidy

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New genetic material can arise as a result of
chromosome duplication (allopolyploidy,
autopolyploidy, aneuploidy)
The frequency of haploid chromosome numbers in
dicotyledonous plants
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• THE ORIGINS OF NEW GENETIC MATERIAL
• Gene Duplication

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New genetic material can arise as a result of
gene duplication
pseudogenes
order of appearance during development
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New genetic material can arise as a result of
gene duplication
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New genetic material can arise as a result of
gene duplication
zeta beta
gamma epsilon
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Phylogenetic tree of relationships among the
globin genes
600-800myo
450-500myo
gt300myo
150-200myo
260myo
100-140myo
40-50myo
40-80myo
35myo
a1
?a1
T1
?
e
G?
A?
d
ß
myoglobin
a globin family chromosome 16
ß globin family chromosome 11
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Homeobox genes (HOX Box genes)
Original Hox gene
Original 5 duplications
Drosophila
Mouse Chromosome 6
Mouse Chromosome 11
Mouse Chromosome 15
Mouse Chromosome 21
One of a group of genes with a shared nucleotide
segment that are involved in the formation of
bodily segmentation during embryologic
development.HOX box. Binds to DNA enhancer
regions to regulate development.
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MADS-box genes are DNA-binding transcriptional
activators which regulate developmental processes
in plants The MADS segment (blue) is 56 Amino
Acids in length and binds to DNA. Other segments
are known to interact with other proteins to
control floral development.
1 billion ybp
Type I
Type II
Chara
MIKCc
Mosses Pteridophytes Seed Plants
MIKCc
MIKC
Flowering plants - 12 clades
Further duplications have occurred in each clade
in different angiosperm lineages
AP3 petal stamen
AG (4 genes) carples fruits
SEP1-3 petal stamen carpel
AGL6
AGL12
AP1 sepal petal
FLC flowering inhibition
AGL17 roots
STMADS11 floral promoter
AGL15 embryo
B-sister
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• CHANGE IN FUNCTION OF GENETIC MATERIAL CAN
  PRODUCE EVOLUTIONARY NOVELTIES

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• New functions occur as a result of
• Mutation resulting in a change in one or more
  amino acids that alters function
• Changes in regulatory functions such that genes
  are transcribed at different times or in
  different tissues
• Duplicated DNAs may change function and are free
  to drift since the original gene retains function

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INCREASING EVIDENCE SUGGESTS THAT CHANGES IN
EUKARYOTE DEVELOPMENT ARE DUE TO CHANGES IN
REGULATION PATTERNS MORE THAN CHANGES IN PROMOTER
SEQUENCES
CHANGE IN TIMING, SHAPE OF FLOWER ETC
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Structural homology of the genes for hen lysozyme
and goat lactalbumin Change in Function
nutritional component of milk
a protective enzyme that breaks down bacterial
membranes
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Change in Function
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Two parallel signaling pathways The signaling
pathway that activates Drosophila DL morphogen
parallels a mammal signal pathway that activates
NFkB, a transcription factor active in antibody
production
Mechanisms for developmental regulation are old
and tightly conserved.
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• MOLECULAR CLOCKS

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MOLECULAR CLOCKS
Can the number of mutational differences be used
to estimate time of divergence? Given a number
of caveats, the answer is yes but the clock must
be calibrated with known fossil evidence or known
vicariance events
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Synonymous changes refer to a mutation which
substitutes the same amino acid
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(No Transcript)
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• COMPARATIVE GENOMICS AND PROTEOMICS
• Genetic evidence of common ancestry

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The distribution of eukaryotic proteins according
to broad categories of biological function
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The distribution of human proteins according to
the identification of significantly related
proteins in other species
Ancient genes
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Figure 19-23

• A synteny map of the human genome

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• The Neanderthal People

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Sequencing Neanderthal DNA from a metagenomic
library
New finds in Gibraltar date Mousterian tools to
as recently as 28,000 ybp. By inference, their
Neanderthal makers survived in southern Iberia
long after all other well-dated occurrences of
the species Nature 19 Oct 2006
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Sequencing Neanderthal DNA from a metagenomic
library
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A gene associated with human speech and a gene
associated with red hair and fair skin have been
isolated from two samples of Neanderthal Man DNA
Light skin was predicted by evolutionary theory
which posits that light skin is an adaptation to
vitamin D deficiency in northern latitudes
Reconstruction from French fossil Science Vol
318546 (2007)
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Sequencing Neanderthal DNA from a metagenomic
library
Vindija cave in Croatia (pictured below) kept a
38,000-year-old Neanderthal fossil relatively
free from human and biological contamination.
Contamination rate was 5
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Sequencing Neanderthal DNA from a metagenomic
library

• DNA was extracted from a 38,000 year old specimen
• 65,250bp of DNA was recovered, averaging 52bp in
  length (ancient DNAs are degraded
• Used a new technique for sequencing directly from
  genomic DNA called pyrosequencing
• together with standard Sanger sequencing Science
  314 1113-1118 17 Nov 2006

DNA divergence was 0.5
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• END