Chapter 7- Molecular Evolution

utility of molecular evolution

• used to combat disease; ‘host switch’ diseases deadly since human immune sys. doesn’t recognize

• #1 goal: identify reservoir using evol. comparisons of molecular sequences

molecular evolution

study of relationships between structures of DNA, RNA, proteins, and organim’’s function

genome

organism’s full set of genes + noncoding DNA (humans- 3.2 billion nucleotides; ~20k genes)

• in eukaryotes, genetic material in nucleus + mitochondria & chloroplasts (where present)

mutation

any change in genetic material; necessary ingredient of evolution, two types

non-synonymous mutation

• change protein function

• classify effect on fitness as beneficial, neutral, or harmful

synonymous (silent) mutation

• do not change protein function

• more common than nonsynonymous

“large scale” change in chromosome structure

what may occur during crossing over?

neutral theory of molecular evolution

• kimura,1968

• most mutations at molecular level are neutral (=no fitness change) accumulate through genetic drift, not NS

  • includes much variation w/in & b/w species

  • offshoot of modern evolution synthesis

what does the neutral theory of molecular evolution NOT suggest?

organsims not adapted, ALL variation is neutral, or NS is unimportant (compatible w/ evol. by NS)

duplications

• can involve genes…entire genome

• Ohno argued that these were the most important evolution events since last common ancestor

• primary mechanism for evolution of complexity in higher organisms?

importance of gene duplication

• common (50% of genes in human genome have multiple copies)

  different homologies: orthology vs paralogy

• give rise to gene families (few to 100s): non-identical sequences, genes or pseudogenes possible

  • contiguous clusters on chromosomes or scattered in genome

  • homeotic genes: specific #, placement of segments during embryo development (hox); mutations may greatly alter

possible outcomes of gene duplication

• both retain function; more gene product

• both retain function; expression change in tissues, time of development

• 1 incapacitated by mutation; functionless pseudogene

• *1 original; 2nd new function

novel functions possible in gene duplication

• “extra” genes free from selective pressure

  • ex. fish: produce electric signals; through changes in duplicated Na⁺ channel genes (normal use: muscle contraction)

gene regulation

• turns genes on/off

• any step of gene expression may be altered [DNA-RNA transcription to post-trans. modification]

• regulatory mutations may play larger role in diff. among spp. vs structural gene changes

  • ex. antarctic icefishes produce antifreeze & other ‘helper’ proteins in large amnts (=upregulated) * genes present, not expressed in warm water relatives

convergent molecular evolution

• lysozyme: enzyme found in most animals; 1st line of defense against bacteria (digests, ruptures cell wall)

• also used in cellulose digestion (new, non-defensive role)

• - mammals: foregut fermentation evolved 2x independently

• birds too (hoatzin: tropical leaf eater)

change in DNA with evolution of complex morphology

challenge of evolutionary bio is to link..?

human genome (2001) vs pufferfish (2002)

• last common ancestor ~ 450 mya, much conserved (shared 75% of genes), extensive rearrangements, much repetitive DNA in human

human genome (2001) vs mouse (2002)

• LCA 75 mya, 99% genes shared

  • 300 unique genes

  • 1200 vs 550 functional olfactory receptor genes

human genome (2001) vs chimp (2005)

• LCA <10mya, 1% fixed diff. in nucleotides, insertions and deletion (gene expression important)

horizontal gene transfer in evol.

• complicates matters

• likely prevalent in early history of life; continues today among pro-&eukaryotes

• early phylogenies (rRNA genes): archaea+eukarya sister

• by 2005, 225 microbial genomes sequenced- bacteria and archaea genes in same organism

vertical gene transfer

phylogenies are USUALLY based on assumption of…?

nuclear DNA vs organelle DNA (seperate evol. origins)

• rRNA: highly conserved across TOL; useful at domain, kingdom…family (depends on group)

• microsatellites: DNA sequence repeats scattered in genome, highly variable; useful spp…pop…ID individuals; paternity [forensics- FBI]

mitochondrial DNA (mtDNA)

• ~4x faster change vs nuclear

• usually show maternal inheritance

  • why? haploid (1 copy) & maternal (1/2 # indiv.)

• variable among closely related spp (pops.)

• abundant in cells, easier to detect, esp. in ancient samples (ex. neanderthals, museum skins)

chloroplast DNA (cpDNA)

all land plants (mtDNA low utility)