Evolution What causes evolution? Speciation & hybridization. Uncovering evolutionary history

Evolution

What causes evolution?

Speciation & hybridization.

Uncovering evolutionary history.

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.

All these plants are the same species:Brassica oleracea

Mutation: Generation of new alleles:

Point mutations (changing one base to another, e.g., C-->T)

• unrepaired DNA damage, e.g. from UV-light, chemicals

• uncorrected copying errors: in any system, error-freetransmission of information is a theoretical impossibility

• Mutations that are transmitted into gametes areevolutionarily important

Sickle cell anemia is an example of a point mutation causing a big change in phenotype.

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

• Why?1. Most of the genome seems to be ‘junk’ -- at least it doesn’t 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 don’t change the amino acid specified. I.e., there is redundancy in the genetic code

Q: What are the consequences of mutations for an individual’s ability to survive and reproduce?A: Most mutations have no effect or almost no effect.

For example, 6 different codons specify the amino acide leucine.

This distribution of the fitness effects shows:

• most s 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 s are beneficial so conservation of genetic variation is extremely important. Fitness











Gene flow tends to homogenize populations. Rates of gene flow depend on the spatial arrangement of populations.

More models of gene flow






Founder effect: Gene flow and genetic drift are responsible for the limited genetic variation on islands,

relative to mainland populations.

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

Convergent structures in the ocotillo (left) from the American Southwest, and in the

allauidia (right) from Madagascar.

This, believe it or not, is a South African member of the milkweed family.

QuickTime™ and aPhoto - JPEG decompressor

are needed to see this picture.

alpine clover and forget-me-nots -- convergence in growth habit

Nectar feeders have converged on this hovering long-tongued

morphology.

Another animal example of convergence.

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 can’t mate with parents– If hybrids not fit and parents waste resources

making them then selection could act to minimize hybridization.

Most dandelions are asexual. So the biological species concept doesn’t apply.How can you name species depending on who can mate with whom when the organisms do not mate at all?!

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.

A. syriacaA. syriacaA. speciosa

These milkweeds hybridize in the central plains.

hybrid

Scarlet and Black oaks can hybridize

and inhabit the same range -- but

they have different microhabitat

preferences and so hybridization is

rare.

These pines can also hybridize but they shed their pollen at different times of the season

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.

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 => 4n(Normallyn x n => 2n)

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.

Geographical isolation leads to genetic differences among the different populations.

Theorem: geographic isolation is necessary for new species to arise.

Counter-theorem: strong natural selection or big mutations can cause divergence within populations.

Taxonomy vs. Systematics• Taxonomy

– discovering– describing– naming– classifying

• Systematics– Figuring out the evolutionary

relationships of species to each other.

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.

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.

Modern taxonomic groups generally correspond to clades on a phylogenetic tree (=cladogram)

plant taxonomy

taxon - any group at any rank

speciesgenusfamilyorderclassdivision (phylum)kingdom

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”

" ironweed "

" ironweed "

Genus - always capitalized

Acer rubrum - red maple

species - not capitalized

- either italicized or underlined

Acer rubrum : the scientific name the Latin name

the genus & species name

Carolus Linnaeus (born Carl von Linné)

- wrote Species Plantarum in 1753

- first use of binomial nomenclature

- named 7,300 species

My academic lineage can be traced back to Linnaeus …

… and now, so can yours.

Systematic relationships are illustrated on a phylogenetic tree

This tree is not cladistic either. Extant groups seem to give rise to other extant groups.

For example, human ancestors are not the apes we know now.

Gorillas Chimps Humans

Common ancestor of chimps and humans

present

time

We need fossils to look back in time for morphological traits --


Australopithicus

present

time

Neanderthal

-- and even then we’re not sure where to put the fossils on the tree.


Australopith

icus

present

time

Neanderthal

Angiosperm Phylogeny Group tree.

“Dicots” are not a monophyletic

group.

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

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.

Distance-based approaches begin with comparing each taxon to every other taxon…

Sp1 Sp2 Sp3 Sp4 Sp5

Sp1

Sp2

Sp3

Sp4

Sp5

0

0

0

0

0

d12 d13 d14 d15

d25

d35

d45

d24

d34

d23…to estimate a“distance matrix”

Distances are then ‘clustered’ to estimate a phylogenetic tree.

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

Many kinds of data are appropriate for the distance matrix, then clustering approach.

– 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

Parsimony and ML approaches use a different data structure.

Species 1

Species 2

Species 3

Species 4

Species 5

trait1 trait52 3 4

0

0

1

1

1

1.2

3.4

3.5

4.0

2.8

red

blue

red

red

blue

Traits musthave discretecharacterstates.

A

G

A

A

G

T

C

T

T

T

Using only trait 1 …

Species 1

Species 2

Species 3

Species 4

Species 5

trait1 trait52 3 4

0

0

1

1

1

1.2

3.4

3.5

4.0

2.8

red

blue

red

red

blue

A

G

A

A

G

T

C

T

T

T

trait1:0<->1

sp1 sp2

sp3sp4sp5

But traits 3 & 4 disagree with trait 1. Trait 5 is no help.

Species 1

Species 2

Species 3

Species 4

Species 5

trait1 trait52 3 4

0

0

1

1

1

1.2

3.4

3.5

4.0

2.8

red

blue

red

red

blue

A

G

A

A

G

T

C

T

T

T

sp5 sp2

sp1 sp4sp3

Red<->blueA<->G

Since two traits (blue, G) suggest the left tree it is more parsimonius than the right

tree, which is based on one trait (0).

2 5 1 3 4

Blue

RedA

G

0 0

1

21 3

Blue

A

G

0

1

54

Red

BlueG

Maximum likelihood begins with a model of nucleotide substitution

A C G T

A

C

G

T

P(A) P(A->C) P(A->G) P(A->T)

P(C)

P(G->C)

P(T->C)

P(C->G)

P(G)

P(T->G)

P(C->T)

P(G->T)

P(T)

P(C->A)

P(G->A)

P(T->A)

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

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Evolution What causes evolution? Speciation & hybridization. Uncovering evolutionary history