what we will cover: kinds of variation where new alleles come from where new genes come from rates...

What we will cover:• Kinds of Variation• Where new alleles come from• Where new genes come from• Rates of mutation

Sources of variation – Chapter 5

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Kinds of Variation

1. Genetic

2. Environmental

3. Genotype x environment interaction

Kinds of Variation

1. Genetic

• The Machinery of Life

• Genetic Variation

1. Environmental

2. Genotype x environment interaction

Representative examples of environmentally induced alternative phenotypes (polyphenism). (a) Normal (left) and predator-induced (right) morphs of water fleas, Daphnia cucullata (photo courtesy of Ralph Tollrian); (b) wet-season (top) and dry-season (bottom) gaudy commodore butterflies, Precis octavia (photo courtesy of Fred Nijhout); (c) omnivore (top) and carnivore-morph (bottom) spadefoot toad tadpoles, Spea multiplicata (photo by David Pfennig); (d) small-horned (left) and large-horned (right) dung beetles, Onthophagus nigriventris (photo by Alex Wild); (e) broad, aerial leaves and narrow, submerged leaves (circled) on the same water crowfoot plant, Ranunculus aquatilis (photo by John Crellin/FloralImages).

David W. Pfennig , Matthew A. Wund , Emilie C. Snell-Rood , Tami Cruickshank , Carl D. Schlichting , Armin P. Mocz... Phenotypic plasticity's impacts on diversification and speciation

Trends in Ecology & Evolution, Volume 25, Issue 8, 2010, 459 - 467 http://dx.doi.org/10.1016/j.tree.2010.05.006

Environmental Variation – Phenotypic plasticity

Phenotypic plasticity – when an individuals phenotype is influenced by the environment.

Induction of the “crown of thorns” in the D. atkinsoni species complex exposed to chemical cues released by Triops cancriformis.

Petrusek A et al. PNAS 2009;106:2248-2252©2009 by National Academy of Sciences

Environmental Variation – Phenotypic plasticity

Induction of the “crown of thorns” in the D. atkinsoni species complex exposed to chemical cues released by Triops cancriformis. This notostracan is portrayed on an Austrian stamp as “the most ancient extant animal species”. (A) Induced Daphnia show a distinctly enlarged carapace extension into the head shield, forming heart-shaped lobes lined with strong spines (B: lineage 1, whole body SEM image; C Left: lineage 3, head). Noninduced individuals exhibit inconspicuous lobes without thorns (C Right: identical clone of lineage 3)

"Triops cancriformis2" by Stijn Ghesquiere at the English language Wikipedia. Licensed under CC BY-SA 3.0 via Wikimedia Commons - http://commons.wikimedia.org/wiki/File:Triops_cancriformis2.jpg#mediaviewer/File:Triops_cancriformis2.jpg

Tadpole shrimp

Phenotypic plasticity – when an individuals phenotype is influenced by the environment.

Inducible defense

Predator cue induction experiments.

Petrusek A et al. PNAS 2009;106:2248-2252

©2009 by National Academy of Sciences

Lineage #3

Lineage #1

Environmental Variation

Examples of phenotypic plasticity abound.

Are they important to the process of evolution?

Experiments are with Daphnia clones, which are genetically identical.

Since Daphnia are genetically identical, the presence of a “crown of thorns” (or neck teeth in textbook) is not passed on by genes from one generation to the next. The trait is determined by the environment (the presence of a substance – a kairomone).

What is a kairomone? A chemical released into the environment that benefits the receiver, but has either a neutral or negative impact on the emitter.

Genotype by Environmental Interactions

Because phenotypic plasticity is a heritable trait

An organism that develops different phenotypes in different environments is said to exhibit phenotypic plasticity.

Why are environmentally induced traits interesting from an evolutionary standpoint?


In Leopard geckos (Eublepharis macularius), the sex of the offspring is determined by the incubation temperature of the eggs.


Different paternal families (n = 12) respond differently to incubation temperature.

The sex (sex ratio in this study) varies among males.

% m

ales

Reaction Norm – The pattern of phenotypes an individual (genotype) may develop upon exposure to different environments.

Multiple reaction norms.


A heat shock shortly before molting produces larvae of tobacco hornworm (Manduca sexta) of different shades of black -> green.


Because the degree to which a phenotype responds to the environment is genetically controlled, phenotypic plasticity can be selected for.

Selection for different degrees of plasticity…

…results in lineages with different reaction norms.


Because the degree to which a phenotype responds to the environment is genetically controlled, phenotypic plasticity can be selected for.

Selection for different degrees of plasticity…

…results in lineages with different reaction norms.

Because phenotypic plasticity is a heritable trait, it forms the raw material for evolution to act on.

Where New Alleles Come From

Mutation – An error in the replication of a nucleotide sequence, or any other alteration of the genome that is not manifested as reciprocal recombination.


Basic mutations in alleles come from errors in the DNA that escape repair before or during replication.

Errors made during replication may go uncorrected, and may escape repair afterward.


A mutation (spontaneous deamination) to the DNA that is not repaired during replication.


A mutation (spontaneous deamination) to the DNA that is not repaired during replication.

Will become fixed if it is not repaired before the next replication.

A permutation – an alteration still susceptible to repair.


Point mutations can be classified by the type of change to the DNA sequence transitions = replace purine with purine (A for G), pyrimidine with pyrimidine (T for C).transversions = replace purine with pyrimidine (T for G) and vice-versa.

Transitions are 2x more common than transversions.


Point mutations can be classified by the type of change to the DNA sequence transitions = replace purine with purine (A for G), pyrimidine with pyrimidine (T for C).transversions = replace purine with pyrimidine (T for G) and vice-versa.

Transitions are 2x more common than transversions.

PyrimidinesPurines


Fitness effects of point mutations - Overall, the effect of a point mutation can range from highly beneficial to very harmful (deleterious).


Replacement substitution (nonsynonymous, or missense) – a base substitution that causes a change in the amino acid.


Silent site substitution (synonymous) – a base substitution that does not cause a change in the amino acid due to codon redundancy.

• Because of the structure of the genetic code, most synonymous mutations occur in the third base position of the codon.

• Approximately 70% of changes in the third position are synonymous, whereas all changes in the second, and most (96%) at the first position are meaningful (nonsynonymous).


Nonsense mutation -


A frameshift mutation. This changes the reading frame, so all codons after the point of mutation are affected:

Most frameshift mutations will have large effects – usually negative.

It is fairly common for frameshift to result in premature stop codon (nonsense mutation) – so resulting protein may be completely non-functional.


A frameshift mutation. This changes the reading frame, so all codons after the point of mutation are affected:

a. additions = extra base inserted

b. deletions = base is “missed”

These collectively are known as indels.

(indel = insertions + deletions)

Where New Alleles Come FromThe fitness effects of a mutation will also depend on environmental conditions as well.

e.g.: sickle-cell anemia.

Where New Genes Come From

A karyotype (from Greek κάρυον karyon, "kernel, seed or nucleus", and τύπος typos, "general form") is the number and appearance of chromosomes in the nucleus of a eukaryotic cell.(Wikipedia)

Often described as a picture of an individual’s chromosomes.

Alterations of the karyotype fall into two major categories:• Rearrangements of one or more chromosomes. These are caused by breaks in

the chromosome, followed by rejoining of the pieces in new configurations.• Changes in the number of wholes sets of chromosomes – polyploidy.


Chromosome rearrangements include:• Deletions or deficiencies• Inversions• Duplications• Translocations• Fissions and fusions


Gene Duplications - are either short or long segments of extra chromosome material originating from duplicated sequences within a genome.

Unequal crossing over – an error during genetic recombination (meiosis) when two chromosomes are not perfectly aligned.

The incorrect alignment can occur when a transposable element has been inserted at multiple loci.

Transposable element (transposons) – Any DNA sequence capable of transmitting itself or a copy of itself to a new location in the genome.


Gene Duplications – Unequal crossing over

• Each locus codes for a polypeptide (protein subunit) of hemoglobin.

• Two of the protein subunits come from the α-like cluster and two of the protein subunits come from the β-like cluster.

• Each locus is expressed during a different time in human development– functions differ enough to make each locus well-adapted for a different stage of development

The globin gene family = two clusters of loci coding for component subunits of hemoglobin:

α-like cluster on chromosome 16 includes 3 functional lociβ-like cluster on chromosome 11 includes 5 functional loci


Test hypothesis that the loci within the gene cluster arose via duplication.

Prediction #1 = should get fairly high degree of structural and functional similarity.

3 lines of evidence support the hypothesis:

Each locus is expressed during a different time in human development– functions differ enough to make each locus well-adapted for a different stage of development.


Prediction #1 = should get fairly high degree of structural and functional similarity.

3 lines of evidence support the hypothesis:

1) high structural similarity of transcription units among loci, including position and length of introns and exons

2) high sequence similarity among loci

3) similarity in function


Prediction #2: Not all duplicated genes will have accumulated favorable mutations – should see some loci that are non-functional (“failed experiments”).

Supported by presence of pseudogenes = non-functional lengths of DNA (but with some structural similarities)


Gene Duplications – Retroposition (retroduplication)

Occurs when processed messenger RNA (lacking introns) is reverse transcribed to form DS-DNA.

If the new DS-DNA is inserted into a chromosome, it becomes a duplicate gene (pseudogene).

Often non-functional because the new segment of DNA lacks the nearby regulatory sequences that cause it to be transcribed.


Gene Duplications – Footprints in the genome

Genes created by unequal crossing over:

• Contain the same introns as the parental genes.

• Found in tandem on the same chromosome.

Genes created by retroposition:

• Lack introns.

• Found far from original gene.


Chromosome mutations

• Inversions

• Genome duplication



Inversions – when a chromosome segment breaks in two places and reanneals with the internal segment reversed.

Individual organisms may be homozygous or heterozygous for a rearranged chromosome.

Homokaryotype – both chromosomes are affected.Heterokaryotype – only one chromosome is affected.



Inversions affect the degree of linkage among alleles.

linkage = tendency of alleles to be inherited together.


Inversions generally lower the recombination frequency within the inverted sequence, because crossing over within such sequences in heterozygotesrequires ‘looping’, and this can lead to chromosomal abnormalities.

Genes in the loop tend to remain together as a nonrecombinant block, called a supergene.


Homokaryotypes can cross-over normally and gamete formation is unaffected, but…

…in heterokaryotypes, fertility may be reduced because many gametes are inviable because the chromosome lacks a centromereOther chromosomes are missing genetic information, and are also inviable.



Genome duplication – duplication of entire sets of chromosomes.

Occurs as an error during:Meiosis I Meiosis II

Failure to segregate

Failure to separate

Offspring are polyploidy through self-fertilization with diploid gametes.


Euploid variation- an entire set of chromosomes is duplicated once or several times.Since most reproducing eukaryotes are diploid, with two sets of chromosomes (2n), euploid variations may extend from the haploid or monoploid condition (1n) to various levels of polyploidy.


How polyploids develop

Autopolyploidy - the appearance of extra sets of chromosomes within a species itself.

Common in plants – mosses, apples, pears, bananas, tomatoes, corn


How polyploids develop

Allopolyploidy- polyploids that originate from crossing between different species.

Appears in such plants as wheat.


Polyploidy is common among plants. Estimates of the proportion of polyploidy angiosperms ranges from 30% to 50-70%.

a. Polyploid formation in plants is very high – possibly as high as the rate of point mutations.

b. Majority of polyploidy plants are allopolyploids (from closely related species) and they usually present a mixture of traits or an intermediate condition of their parents.


Polyploidy is much rarer in animals than in plants, because animals show much greater developmental sensitivity to even a small change in chromosome number.

Maintaining the same proportions of X and Y chromosomes present in normal diploids is difficult for animals.

Males which are XY and females are XX could lead to establishment of XXYY males and XXXX females.

The subsequent combination of gametes produced by these individuals (XY sperm + XX eggs) might produce XXXY individuals that are not completely female or male.


Kleinfelter’s syndrome

Turner’s syndrome


Down’s syndrome

Trisomy at chromosome #21.

When animal polyploidy species do occur, they usually have some form of asexual reproduction, such as parthenogenesis (embryonic development of eggs without fertilization).

Aneuploid variation – the abnormal condition were one or more chromosomes of a normal set of chromosomes are missing or present in more than their usual number of copies.

E.g. if an otherwise diploid organism has three copies of one its chromosomes -> Down’s syndrome.


Huge amounts of duplication in the humane genome.

- ~5% consists of copies longer than 1,000 bp.

- ½ chromosome 20 recurs in a rearranged state on chromosome 18.

- A large block of chromosome 2’s short arm appears as ¾ of chromosome 14 ,

and a section of its long arm appears on chromosome 12.

Measuring Genetic Variation in Natural Populations

Mean heterozygosity = % of heterozygous loci in the average individual.

1. Measure variation across loci within an individual, 2. Then averaged across population

1) AaBbCCDD2) AABBCCDD3) AAbbCCDD4) aabbCCDD

2 heterozygous loci/ 4 loci total = 50% heterozygosity




50%/4 = 12.5 mean heterozygosity

Measuring Genetic Variation in Natural Populations

Percent polymorphism = % of loci in the population that have at least two alleles. Measure variation within the population as a whole.

1) AaBbCCDD2) AABBCCDD3) AAbbCCDD4) aabbCCDD

Number of loci in the population =

Number of loci that are polymorphic -

2/4 = 50% polymoprphism

4 – A, B, C, D

2 – A & B

Mutation Rates

The mutation rate is a measure of the frequency of a given mutation per generation (or per gamete, which is equivalent). • Ordinarily, rates are given for specific loci. • Thus the mutation rate for achondroplasia (short stature) is 6-13 mutants per

million gametes. • This means that each gamete has ca. 1 chance in 100,000 of carrying a new

mutation for achondroplasia.

Mutation Rates

what we will cover: kinds of variation where new alleles come from where new genes come from rates...

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