Table 8.3 & Alberts Fig.1.38

EVOLUTION OF GENOMES

C-value paradox: - in certain cases, lack of correlation between morphological complexity and genome size

“[For] some commonly cited extreme values for amoebae... considerable uncertainty about the accuracy of these measurements and the ploidy level of the species...” Gregory Nature Rev. Genet. 6:699, 2005

Fig. 8.15

Genic fraction vs. genome size

Function of non-genic DNA in eukaryotes?

Gregory Nature Rev. Genet. 6:699, 2005

Composition of human genome

Hartwell Fig. 21.11

Genic contribution to expansion in genome size

Figure 8.7

Scenario showing possible events following whole genome duplication

26 genes on 2 chromosomes

36 genes on 4 chromosomes

Kellis Nature 428:617, 2004

Evidence for whole genome duplication in ancestor of yeast

see also Fig.8.7

~ 100 million years ago?

Frequency distribution of haploid chromosome numbers in dicot plants

For chromosome number >12, even numbers much more common than odd numbers

Griffiths 7th ed, Fig. 26-12

Duplication of entire genome much more common in plant evolution than in animal evolutionary history

Fig. 6.25

Over evolutionary timeexpect independent mutationsto accumulate

Evolution of tandem arrays of eukaryotic genes

… but often observe all copiesidentical (or nearly so)

- evolve “in concert”

Concerted evolution

- maintenance of homogeneous nt sequences among multi-gene family members (especially when in tandem arrays)

- eg. eukaryotic ribosomal RNA gene copies

- exchange of sequence info so members kept very similar

Fig. 6.26

Fig. 6.27

Possible evolutionary scenarios resulting in “homogenized” tandem array

1. Beneficial mutations fixed by positive selection

-but spacers with no known function show concerted evolution

2. Recent amplification

3. Mutation in one repeat “spreads” to others

Fig. 6.31

Unequal crossing over

- homologous recombination between misaligned arrays

- change in number of repeats

Example of unequal crossing over in human globin array

misalignment (of sister chromatidsduring mitosis in germ cell orhomologous chromosomes during meiosis…)

Page & Holmes Fig. 3.15

“Lepore” thalassemia

Gene conversion

- non-reciprocal recombination

- no change in gene copy number

- can occur in dispersed as well as tandem repeats

Fig. 6.29 Watson Fig. 10-21

- example of yeast mating-type switching

Fig. 6.33

Exon 3 Exons 1 & 2

How do you interpret these data?

Example of concerted evolution in primate globin gene cluster

... and panel 3 of Fig.6.33 ?

Fig. 6.33

PR pancreative ribonuclease

SR seminal ribonuclease

Resurrection of ribonuclease pseudogene by gene conversion

What is predicted status of SR gene in giraffe? or sheep?

… in some bovine species, gene conversion of SR with PR gene, so functional again

Factors affecting rate of concerted evolution (p. 317-320)

1. Number, arrangement, structure of repeats

2. Functional requirement

- selective advantage of high amount of same geneproduct vs. diversity

3. Population size

- non-coding regions evolve more rapidly, and ifdivergent enough may “escape” homogenization

- time for variant to be fixed or eliminated

Evolutionary implications of concerted evolution (p.320-322)

1. Spread of advantageous mutations (or removal of deleterious ones)

2. Retards paralogous gene divergence (preventing redundant copy from becoming non-functional)

3. Generates increased genetic variation at a particular locus within a population

“molecular drive”

Methodological implications

- degree of sequence divergence of paralogous genes undergoing concerted evolution is not correlated with evolutionary time

so gene duplications can appear younger than they really are…