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 AlignmentFigure 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

LangursFigure 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 changesFigure 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

C-value

Inflation

Figure 26.8

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 phylogeneticsreconstructs 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