TOPIC FOR DISCUSSION TO-DAY:

1. THE C VALUE PARADOX

QUESTIONS FOR DISCUSSION:

Why do genome sizes vary by so many orders of 
magnitude among different organisms?

Why does the gene coding fraction of the genome also 
vary so widely among organisms?

Can genome size be related to any particular phenotypic 
or morphological attributes?

Are there maximum and minimum constraints imposed 
on genome size by natural selection?

Do noncoding regions of the genome serve any function 
at the individual organism level or at the individual 
species level? 

2. CONCERTED EVOLUTION

QUESTION FOR DISCUSSION:

Why are members of some multigene families much more 
similar to one another within a species than they are between 
closely related species?


Reading assignment:

Futuyma Chapter 22.

Additional reference:

Li, W-H. 1997 Molecular Evolution. Sinauer Associates, Sunderland MA. 
Chapter 10.
BACKGROUND

GENOME ORGANIZATION AND EVOLUTION

C VALUES

The amount of DNA in a haploid genome set (such as in a 
sperm nucleus) is called the genome size or C value 
where C stands for "constant" or "characteristic" to 
denote that C values are relatively constant within a 
single species, but vary widely between species

                                                   

1 kb = 1,000 bp.      1 Mb (or Mbp) = 1,000,000 bp

EVOLUTION OF GENOME size IN BACTERIA
	Nuclear genome: Chromosomal DNA
	Plasmid genome: Plasmid DNA
	Transposable genetic elements
Genome sizes in bacteria vary over a 20-fold range 
	from 6 x 105 bp in some obligatory intracellular parasites
     to more than 107 bp in several cyanobacterial species
                                                  
The smallest free-living prokaryotes, the mycoplasmas, contain about 350 protein-coding genes.

GENOME SIZE IN  EUKARYOTES AND THE C 
VALUE PARADOX

C values are usually much larger in eukaryotes than prokaryotes 
with some exceptions (yeast)

However, the large variation in eukaryotic C values seems to 
bear no relationship to either organismic complexity or the 
likely number of genes coded for by an organism (table 4)

The large interspecific differences are accounted for by DNA 
that is noncoding

Nongenic DNA varies from < 30% to almost 100%

THE REPETITIVE STRUCTURE OF THE 
EUKARYOTE GENOME

MECHANISMS FOR INCREASING GENOME SIZE
	Genome duplication - polyploidy
	Chromosomal duplication
	Regional increases in genome size

The repetitive structure of the eukaryote genome
Two major features:
1. Repetition of sequences
2. Compositional compartmentalization

Repetitive DNA
 Divided into several classes according to degree of repetitiveness:
a. Foldback DNA -pallindromic sequences
b. Highly repetitive DNA short sequences repeated an average of 500,000 times
c. Middle repetitive DNA
d. Single copy sequences

Repeated sequences can be localized (tandem repeats) or dispersed in the 
genome

Insert Fig.

                                                   


MAINTENANCE OF NONGENIC DNA
	4 hypotheses
1. Performs some essential function such as global regulation of 
gene expression - little evidence
2. Useless "junk DNA" carried passively by the chromosomes 
because of linkage to functional genes - neutral to the 
organism-
3. Functionless parasitic DNA or "selfish" DNA that 
accumulates and is actively maintained by intragenomic 
selection
4. Structural or nucleotypic function unrelated to the task of 
carrying genetic information e.g. nucleoskeleton or 
mechanical function
Different types of nongenic DNA may be maintained by 
different mechanisms

Table 4.     
C values from eukaryotic organisms ranked by genome size.

     Species				C value (kb)

Navicola pelliculosa (diatom)	35,000
Drosophila melanogaster (fruitfly)	180,000
Paramecium aurelia (ciliate)	190,000
Gallus domesticus (chicken)	1,200,000
Erysiphe cichoracearum (fungus)	1,500,000
Cyprinus carpio (carp)	1,700,000
Lampreta planeri (lamprey)	1,900,000

Boa constrictor (snake)	2,100,000
Parascaris equorum (roundworm)	2,500,000
Carcarias obscurus (shark)	2,700,000
Rattus norvegicus (rat)	2,900,000
Xenopus laevis (toad)	3,100,000
Homo sapiens (human)	3,400,000
Nicotiana tabaccum (tobacco)	3,800,000
Paramecium caudatum (ciliate)	8,600,000
Schistocerca gregaria (locust)	9,300,000

Allium cepa (onion)	18,000,000
Coscinodiscus asteromphalus (diatom)	25,000,000
Lilium fomosanum (lily)	36,000,000
Amphiuma means (newt)	84,000,000
Pinus resinosa (pine)	68,000,000

Protopterus aethiopicus (lungfish)	140,000,000
Ophioglossum petrolatum (fem)	160,000,000
Amoeba proteus (amoeba)	290,000,000
Amoeba dubia (amoeba)	670,000,000


Data from Cavalier-Smith (1985), Sparrow et al. (1972),and other references.


CONCERTED EVOLUTION OF MULTIGENE FAMILIES
	
	Attempts to explain why members of a multigene family 
within a species are much more similar to one another than 
members from closely related species

MECHANISMS:
	
	a. Unequal crossing over - important
	
	b.  Gene conversion- important
	
	c.  Master-slave hypothesis -little evidence
	
	d.  Saltatory replication hypothesis - little evidence
	
	e.  Replication-slippage (Slipped strand mispairing)
	
	f.  (Transposition)

Molecular drive (Dover, 1982)

Insert Figures shoping models of unequal crossing over and gene conversion

There are two types of repeats in the figure - one marked with an asterisk and the 
other unmarked.

Unequal crossing over results in daughter chromosomes having an altered total 
number of repeats - 
	an altered proportion of the two repeat types

Gene conversion changes the frequencies of the two types of repeats in only one 
daughter chromosome and does not alter the total number of repeats in 
either daughter chromosome.

Evolutionary consequences:  Concerted evolution allows the 
spreading of a variant repeat to all gene family members 
within a species - horizontal spreading - a beneficial 
mutation can spread and become fixed in all members