Download Molecular and Genomic Evolution

Molecular and Genomic
Evolution
Getting at the Gene Pool
Figure 26.1
What is Molecular Evolution?
• a change in nucleotide &/or amino acid
sequences over time
– molecular phylogenetics reconstructs
lineages based on molecular differences
Determining and Comparing Sequences
• PCR (Polymerase Chain Reaction)
– rapid amplification of DNA from many
samples
• automated sequencing methods
– rapid determination of sequences from PCR
Sequence
Alignment
Figure 26.2
Determining and Comparing Sequences
• homologous DNA sequences are compared by
alignment
– sequences of closely related groups have
fewer differences
Determining and Comparing Sequences
• sequence changes accumulate at different rates
in different parts of the genome
– regions that encode functional products
change relatively slowly
• synonymous changes are most common
– non-coding regions may change rapidly
Figure 26.3
Determining and Comparing Sequences
• good historical evidence combined with
good molecular evidence give the rate of
change of a sequence
• some polypeptides have relatively constant
amino acid substitution rates over time
Determining and Comparing Sequences
• a sequence with a constant rate of change can
be used as a “molecular clock”
– cytochrome c is in the electron transport
chain in the mitochondrion of all eukaryotes
Figure 26.4
amino acid substitution
rate of cytochrome c
Figure 26.5
The Origin of New Protein Functions
• protein function can change
– lysozyme, an antibacterial enzyme, is found
in most animals.
• tears, saliva, milk, egg whites
– some mammals use lysozyme in foregut
fermentation, a type of digestion
• ruminants
• langurs
Langurs
Figure
26.6
The Origin of New Protein Functions
• protein function can change
– foregut fermentation arose in langurs and
ruminants separately
• each descended from non-fermenting
recent ancestors
– langur and ruminant lysozymes share
changes that protect them from digestion
Table 26.1
The Origin of New Protein Functions
• protein function can change
– langur and ruminant lysozymes share
changes that protect them from digestion
– the hoazin, a
foregut fermenting
bird, makes a
lysozyme with
similar changes
Figure 26.6
The Origin of New Protein Functions
• protein function can change
– hoazin, langurs, ruminants all share
distinctive amino acid substitutions in the
same enzyme
– therefore…
• they shared a recent common ancestor?
• homoplasy, such as convergent evolution,
is identified by comparison with patterns
of homology.
The Origin of New Genes
• Gene duplication yields new genes
– duplicate genes may change together
• rRNA gene tandem arrays share changes
so that members retain the same sequence
– duplicate genes often change independently
• one copy of the gene is required to
produce a normal product
• a duplicate copy may change its function
by mutation
The Origin of New Genes
• Gene duplication yields new genes
– duplicate genes are homologs
• paralogs are homologs in the same
genome
• orthologs are homologs in different
genomes
– duplication of genes, chromosomes, or
entire genomes can occur
The Origin of New Protein Functions
• duplicated proteins can change without harm
to the organism
– myoglobin, -globin and -globin gene
families arose following gene duplication
• each family experienced later duplications
Figure 26.9
Figure 26.7
Figure 26.8
C-value
Inflation
A Relevant Mystery
• The C-value paradox
– more-complex organisms have more DNA
per genome than less-complex organisms
– more-complex organisms have more genes
than less-complex organisms
– more-complex organisms have much higher
proportions of non-coding DNA
– the non-coding DNA has no known function
Molecular Phylogenetics
• different molecules change at different rates
over time
– rapidly changing molecules
• useful for recently diverged groups
• slow changing molecules for groups that
diverged long ago
Molecular Phylogenetics
• different molecules change sequences at
different rates over time
– the gene for the small ribosomal RNA
subunit changes very slowly
– serves as one of the bases for the three
domain classification of life
Figure 26.10
Molecular
phylogenetics
reconstructs the
history of gene
evolution
Molecular Phylogenetics
• The Big Bird story
– Moas
• large flightless birds
• extinct for ~1000 years
• shared New Zealand with kiwis
• presumed to share a more recent common
ancestor with kiwis than with other large
flightless birds on other continents