Evolution

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Evolution

• What causes evolution?
• Speciation hybridization.
• Uncovering evolutionary history.

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The four forces of evolution

• Mutation -- spontaneous changes in the DNA of
  gametes. Mutations are the result of mistakes in
  DNA replication, exposure to UV or to some
  chemicals (mutagens) and other causes.
  Prerequisite to all other evolution.
• Natural Selection -- genetically-based
  differences in survival or reproduction that
  leads to genetic change in a population.
• Gene flow -- movement of genes between
  populations. In plants this can be accomplished
  by pollen or seed dispersal.
• Genetic drift -- random changes in gene
  frequency. This is very important in small
  populations.

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Brassica oleracea
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Mutation Generation of new alleles

• Point mutations
• (changing one base to another, e.g., C--gtT)
• unrepaired DNA damage, e.g. from UV-light,
  chemicals
• uncorrected copying errors in any system,
  error-free
• transmission of information is a theoretical
  impossibility
• Mutations that are transmitted into gametes are
• evolutionarily important

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Sickle cell anemia is an example of a point
mutation causing a big change in phenotype.
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Point mutations are only one of many kinds of
chance genetic change

• Indels
• (insertions/deletions)
• Cause frame-shifts, usually premature stops
• Chromosomal mutations
• Inversions, translocations, deletions
• Gene duplication
• May lead to new functions
• Polyploidy
• May lead to new species in one step
• Very common in plants

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Tragopogon pratensis is a new species formed by
hybridization between an American Tragopogon and
a European Tragopogon that was introduced about
150 years ago.
T.p. is a polyploid formed by the union of
unreduced gametes -- i.e. 2n x 2n gt
4n (Normally n x n gt 2n)
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Q What are the consequences of mutations for an
individuals ability to survive and
reproduce?A Most mutations have no effect or
almost no effect.

• Why?
• 1. Most of the genome seems to be junk -- at
  least it doesnt code for proteins. We still may
  have a lot to learn here but the empirical
  evidence regarding mutations effects support
  this view.
• 2. Many mutations within protein-coding genes
  dont change the amino acid specified. I.e.,
  there is redundancy in the genetic code

For example, 6 different codons specify the amino
acide leucine.
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This distribution of the fitness effects shows
most ms have no effect (are neutral) the
remainder are usually deleterious the relatively
high freq. of lethals is due to missense
mutations -- those that cause a premature stop
in protein synthesis. Very few ms are
beneficial
Fitness
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The four forces of evolution

• Mutation -- spontaneous changes in the DNA of
  gametes. Mutations are the result of mistakes in
  DNA replication, exposure to UV or to some
  chemicals (mutagens) and other causes.
  Prerequisite to all other evolution.
• Natural Selection -- genetically-based
  differences in survival or reproduction that
  leads to genetic change in a population.
• Gene flow -- movement of genes between
  populations. In plants this can be accomplished
  by pollen or seed dispersal.
• Genetic drift -- random changes in gene
  frequency. This is very important in small
  populations.

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The four forces of evolution

• Mutation -- spontaneous changes in the DNA of
  gametes. Mutations are the result of mistakes in
  DNA replication, exposure to UV or to some
  chemicals (mutagens) and other causes.
  Prerequisite to all other evolution.
• Natural Selection -- genetically-based
  differences in survival or reproduction that
  leads to genetic change in a population.
• Gene flow -- movement of genes between
  populations. In plants this can be accomplished
  by pollen or seed dispersal.
• Genetic drift -- random changes in gene
  frequency. This is very important in small
  populations.

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Gene flow tends to homogenize populations. Rates
of gene flow depend on the spatial arrangement of
populations.
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More models of gene flow
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The four forces of evolution

• Mutation -- spontaneous changes in the DNA of
  gametes. Mutations are the result of mistakes in
  DNA replication, exposure to UV or to some
  chemicals (mutagens) and other causes.
  Prerequisite to all other evolution.
• Natural Selection -- genetically-based
  differences in survival or reproduction that
  leads to genetic change in a population.
• Gene flow -- movement of genes between
  populations. In plants this can be accomplished
  by pollen or seed dispersal.
• Genetic drift -- random changes in gene
  frequency. This is very important in small
  populations.

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Founder effect Gene flow and genetic drift are
responsible for the limited genetic variation on
islands, relative to mainland populations.
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- Some observable manifestations of evolution

homologous traits similar features in
different species due to shared ancestry.
For example, the Pandas thumb.
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The thumb is homologous to a tiny wrist bone in
other bears and other vertebrates.
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Convergence similar features in unrelated
organisms due to evolution of traits that work
in similar environments

• spiny succulent growth habit in deserts
• schlerenchymatous leaves in many families that
  live in dry habitats
• similar flower sizes, shapes colors for
  attracting pollinators have evolved in many plant
  groups.
• low prostrate growth for of high altitude plants

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Convergent structures in the ocotillo (left) from
the American Southwest, and in the allauidia
(right) from Madagascar.
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This, believe it or not, is a South African
member of the milkweed family.
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alpine clover and forget-me-nots -- convergence
in growth habit
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Nectar feeders have converged on this hovering
long-tongued morphology.
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Another animal example of convergence.
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Hybridization (between species)

• Well -- what is a species, anyway?
• Most species were described by their morphology.
• In vertebrates, morphological discontinuities
  generally correspond to fertility barriers. BSC
• In plants, many named species can hybridize.
• Hybridization can lead to
• Homogenization of divergent species
• Production of new species hybrids are better
  than parents and/or cant mate with parents
• If hybrids not fit and parents waste resources
  making them then selection could act to minimize
  hybridization.

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Most dandelions are asexual. So the biological
species concept doesnt apply. How can you name
species depending on who can mate with whom when
the organisms do not mate at all?!
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These two Calochortus have been named as separate
species. But they are interfertile -- should
we combine them as one species? Their ranges do
not overlap so the chance of hybridization in
Nature is very remote.
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These milkweeds hybridize in the central plains.
hybrid
A. syriaca
A. syriaca
A. speciosa
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Scarlet and Black oaks can hybridize and inhabit
the same range -- but they have different
microhabitat preferences and so hybridization is
rare.
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These pines can also hybridize but they shed
their pollen at different times of the season
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Speciation by hybridization
Hybridization often shows how difficult it is to
apply the BSC to plants. The hybrid in this case
is a new species. The rearrangements of its
chromosomes make it /- infertile with either
parent.
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Tragopogon pratensis is a new species formed by
hybridization between an American Tragopogon and
a European Tragopogon that was introduced about
150 years ago.
T.p. is a polyploid formed by the union of
unreduced gametes -- i.e. 2n x 2n gt
4n (Normally n x n gt 2n)
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As the climate becomes drier the desert splits
the range of this hypothetical tree species.
This reduces gene flow between the now isolated
populations and sets the stage for speciation.
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Geographical isolation leads to genetic
differences among the different
populations. Theorem geographic isolation is
necessary for new species to arise. Counter-theor
em strong natural selection or big mutations
can cause divergence within populations.
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Taxonomy vs. Systematics

• Taxonomy
• discovering
• describing
• naming
• classifying
• Systematics
• Figuring out the evolutionary relationships of
  species to each other.

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Taxonomy vs. Systematics

• Taxonomy products are
• descriptions of new species in journals
• Keys
• Entries in floras e.g., Flora of Missouri lists
  all the species found in MO and has keys for
  identifying plants.
• Systematics produces trees that attempt to
  summarize the evolutionary history of a group.
• Usually done with DNA sequences, these days.

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Phylogenetic trees have more information than a
list of names.
E.g., the nine animal phyla are hypothesized to
have the relationships shown at left.
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Modern taxonomic groups generally correspond to
clades on a phylogenetic tree (cladogram)
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plant taxonomy
taxon - any group at any rank species genus f
amily order class division (phylum) kingdom
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discovering describing naming classifying
2 basic rules of naming organisms - each
species name must be a binomial
- all scientific names must be in Latin or
be Latinized
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" ironweed "
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" ironweed "
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Acer rubrum - red maple
Genus - always capitalized
species - not capitalized
- either italicized or underlined
Acer rubrum the scientific name
the Latin name the genus
species name
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Carolus Linnaeus (born Carl von Linné)
- wrote Species Plantarum in 1753 -
first use of binomial nomenclature - named
7,300 species
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My academic lineage can be traced back to
Linnaeus and now, so can yours.
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Systematic relationships are illustrated on a
phylogenetic tree
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This tree is not cladistic either. Extant groups
seem to give rise to other extant groups.
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For example, human ancestors are not the apes we
know now.
Gorillas Chimps Humans
present
time
Common ancestor of chimps and humans
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We need fossils to look back in time --
Gorillas Chimps Humans
present
Neanderthal
Australopithicus
time
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-- and even then were not sure where to put the
fossils on the tree.
Gorillas Chimps Humans
Australopithicus
present
Neanderthal
time
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Angiosperm Phylogeny Group tree.Dicots are
not a monophyletic group.
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There are many kinds of information that can be
used to estimate a phylogeny.

• Types of data
• Crossability
• Uses the Biological Species Concept
• Morphology
• Continuous traits
• Meristic (countable) traits

• Cytology
• Chromosome number
• Chromosome features
• Pairing in hybrids
• Molecular data
• Secondary chemicals
• Proteins
• DNA

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Kinds of DNA data

• DNA/DNA hybridization
• How well do 2 spp. DNAs match as revealed by
  binding kinetics
• Comparison of Bands on a gel, not genes per se
• RAPD, ISSR
• Genetic distance estimates from
• Allele frequencies at many loci (isozymes, SSR)
• DNA sequences, considered as a whole
• DNA sequences, considered site-by-site
• Parsimony the simplest pathway is probably
  correct
• Maximum likelihood specify a model for
  evolution, fit that model to the data use that
  model to make the tree.

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Distance-based approaches begin with comparing
each taxon to every other taxon
d12
d13
d14
d15
to estimate a distance matrix
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Distances are then clustered to estimate a
phylogenetic tree.

• Types of clustering algorithms
• UPGMA
• Fitch-Margoliash
• Neighbor-Joining

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UPGMA example

• Unweighted Pair-Group Method using Arithmetic
  means.

1
2
3
4
5
1
--
0.1715
0.2147
0.3091
0.2326
--
2
0.2991
0.3399
0.2058
3
--
0.2795
0.3943
4
--
0.4289
5
--
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Many kinds of data are appropriate for the
distance matrix, then clustering approach.

• Cytology
• Chromosome number
• Chromosome features
• Pairing in hybrids
• Molecular data
• Secondary chemicals
• Proteins
• DNA

• Crossability
• Uses the Biological Species Concept
• Morphology
• Continuous traits
• Meristic (countable) traits

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Parsimony and ML approaches use a different data
structure.
Traits must have discrete character states.
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Using only trait 1
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But traits 3 4 disagree with trait 1. Trait 5
is no help.
sp2
sp5
Redlt-gtblue
Alt-gtG
sp3
sp1
sp4
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Since two traits (blue, G) suggest the left tree
it is more parsimonius than the right tree, which
is based on one trait (0).
4
2
1
5
3
3
5
2
1
4
Blue
Blue
0
0
G
G
0
Blue
G
Red
Red
A
A
1
1
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Maximum likelihood begins with a model of
nucleotide substitution
A
C
G
T
A
P(A)
P(A-gtC)
P(A-gtG)
P(A-gtT)
C
P(C)
P(C-gtG)
P(C-gtT)
P(C-gtA)
G
P(G)
P(G-gtA)
P(G-gtC)
P(G-gtT)
T
P(T-gtC)
P(T-gtG)
P(T)
P(T-gtA)
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Probabilities are iteratively estimated for all
the transitions in the substitution matrix until
the probabilities are found that best fit the
data.Other parameters often estimated are
rate variation among nucleotide sites, AT/GC
ratio Then the best model of evolution for the
data is used to generate the tree