Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Studying genetic mechanisms of change can provide insight into large-scale evolutionary change An organism’s genome is the full set of genes it contains. In eukaryotes, most of the genes are found in the nucleus, but genes are also present in plastids and chloroplasts. Genes are shuffled in every generation of sexually reproducing organisms via meiosis and fertilization.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Studies of genomic evolution look at the genome of an organism as an integrated whole and attempt to answer questions such as: – How do proteins acquire new functions? – Why are the genomes of different organisms so variable in size? – How has the enlargement of genomes been accomplished?

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Evolution of Genome Size The size and composition of the genomes of many species show much variation. Genome size varies greatly. Across broad taxonomic categories, there is some correlation between genome size and organism complexity. Multicellular organisms have more DNA than single-celled organisms. Generally, more complex organisms have more DNA than less complex organisms.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 26.8 A Large Proportion of DNA Is Noncoding

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The Evolution of Genome Size If only the protein and RNA coding portions of genomes are considered, there is much less variation in size. Most of the variation in genome size is due to the amount of noncoding DNA an organism has.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Figure 26.7 Complex Organisms Have More Genes than Simpler Organisms

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Much of the noncoding DNA does not appear to have a function. But it can alter the expression of surrounding genes.(regulatory genes) Some noncoding DNA consists of pseudogenes (duplicated genes which are nonfunctional). Some consists of transposable elements (repetetive DNA sequences that can move to different locations in the genome)

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Nucleic acids or genes evolve when nucleotide base substitutions occur. Substitutions can change the amino acid sequence, and thus the structure and function, of the polypeptides. By characterizing nucleic acid sequences and the primary structures of proteins, molecular evolutionists can determine how rapidly these macromolecules have changed and why they changed.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Nucleotide substitutions may result in amino acid replacements. Change in the amino acid sequence can change the charges, secondary and tertiary structure of a protein, and thus its function.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

If an amino acid replacement does not make a difference with respect to fitness, the two rates are expected to be similar; the ratio would be close to one. If an amino acid position is under strong stabilizing selection pressure, the rate of synonymous substitutions should be much higher than nonsynonymous. If an amino acid position is under selection for change, the rate of nonsynonymous substitutions should be much higher than synonymous

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The much slower rate of mutation at sites that do affect molecular function is consistent with the view that most nonsynonymous mutations are disadvantageous and are eliminated from the population by natural selection. In general, the more essential a molecule is for cell function, the slower the rates of its evolution.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Evolutionary changes are determined by comparing nucleotide or amino acid sequences among different organisms. The longer two sequences have been evolving separately, the more differences they accumulate. The timing of evolutionary changes can be determined and causes can be inferred.

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Evolutionary Effects of Development Genes Genes that program development control the rate, timing, and spatial pattern of changes in an organism’s form as it develops into an adult

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Changes in Rate and Timing Heterochrony is an evolutionary change in the rate or timing of developmental events It can have a significant impact on body shape The contrasting shapes of human and chimpanzee skulls are the result of small changes in relative growth rates Animation: Allometric Growth Animation: Allometric Growth

Fig (a) Differential growth rates in a human (b) Comparison of chimpanzee and human skull growth Newborn Age (years) Adult Chimpanzee fetus Chimpanzee adult Human fetus Human adult

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Heterochrony can alter the timing of reproductive development relative to the development of nonreproductive organs In paedomorphosis, the rate of reproductive development accelerates compared with somatic development The sexually mature species may retain body features that were juvenile structures in an ancestral species

Fig Gills

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Changes in Spatial Pattern Substantial evolutionary change can also result from alterations in genes that control the placement and organization of body parts Homeotic genes determine such basic features as where wings and legs will develop on a bird or how a flower’s parts are arranged

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Hox genes are a class of homeotic genes that provide positional information during development If Hox genes are expressed in the wrong location, body parts can be produced in the wrong location For example, in crustaceans, a swimming appendage can be produced instead of a feeding appendage

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Evolution of vertebrates from invertebrate animals was associated with alterations in Hox genes Two duplications of Hox genes have occurred in the vertebrate lineage These duplications may have been important in the evolution of new vertebrate characteristics

Fig Vertebrates (with jaws) with four Hox clusters Hypothetical early vertebrates (jawless) with two Hox clusters Hypothetical vertebrate ancestor (invertebrate) with a single Hox cluster Second Hox duplication First Hox duplication

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Changes in Genes New morphological forms likely come from gene duplication events that produce new developmental genes A possible mechanism for the evolution of six- legged insects from a many-legged crustacean ancestor has been demonstrated in lab experiments Specific changes in the Ubx gene have been identified that can “turn off” leg development

Fig Hox gene 6 Hox gene 7 Hox gene 8 About 400 mya Drosophila Artemia Ubx

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Changes in Gene Regulation Changes in the form of organisms may be caused more often by changes in the regulation of developmental genes instead of changes in their sequence For example three-spine sticklebacks in lakes have fewer spines than their marine relatives The gene sequence remains the same, but the regulation of gene expression is different in the two groups of fish

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 25.6: Evolution is not goal oriented Evolution is like tinkering—it is a process in which new forms arise by the slight modification of existing forms

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Evolutionary Novelties Most novel biological structures evolve in many stages from previously existing structures Complex eyes have evolved from simple photosensitive cells independently many times Exaptations are structures that evolve in one context but become co-opted for a different function Natural selection can only improve a structure in the context of its current utility

Fig (a) Patch of pigmented cells Optic nerve Pigmented layer (retina) Pigmented cells (photoreceptors) Fluid-filled cavity Epithelium (c) Pinhole camera-type eye Optic nerve Cornea Retina Lens (e) Complex camera-type eye (d) Eye with primitive lens Optic nerve Cornea Cellular mass (lens) (b) Eyecup Pigmented cells Nerve fibers

Concept 26.4: An organism’s evolutionary history is documented in its genome Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago mtDNA evolves rapidly and can be used to explore recent evolutionary events

Another way that genomes evolve is by gene duplications. Copies may have one of four fates: 1.Both copies retain original function (more protein product could be made). 2.Both copies retain original function but expression diverges in different tissues or at different times. 3.One copy becomes nonfunctional from accumulation of deleterious substitutions and becomes a pseudogene. 4. One copy accumulates substitutions that allow it to perform a new function. Gene duplication may involve part of a gene, a single gene, parts of a chromosome, or whole chromosomes.

Gene Duplications and Gene Families Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes Like homologous genes, duplicated genes can be traced to a common ancestor

Orthologous genes are found in a single copy in the genome and are homologous between species They can diverge only after speciation occurs

Paralogous genes result from gene duplication, so are found in more than one copy in the genome They can diverge within the clade that carries them and often evolve new functions

Fig (b) Paralogous genes (a) Orthologous genes Ancestral gene Paralogous genes Ancestral species Speciation with divergence of gene Gene duplication and divergence Species A after many generations Species A Species B Species A Orthologous genes

Genome Evolution Orthologous genes are widespread and extend across many widely varied species Gene number and the complexity of an organism are not strongly linked Genes in complex organisms appear to be very versatile and each gene can perform many functions

Successive rounds of duplication and mutation can result in gene families, such as the globin gene family. Amino acid sequencing of globins suggests they arose via gene duplications

Concept 26.5: Molecular clocks help track evolutionary time To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

Neutral Theory Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection It states that the rate of molecular change in these genes and proteins should be regular like a clock The neutral theory of molecular evolution: The majority of mutations are neutral, and accumulate through genetic drift. If a mutation confers an advantage, it quickly becomes fixed in a population.

Using the rationale that the rate of fixation of mutation is theoretically constant and equal to the neutral mutation rate, the concept of the molecular clock was developed. The concept of the molecular clock states that macromolecules evolving in different populations should diverge from one another at a constant rate. The number of changes in these molecules can determine when the species diverged. A molecule that illustrates this principle is the enzyme cytochrome c, a component of the respiratory chain in mitochondria.

Molecular Clocks A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated

Fig Divergence time (millions of years) Number of mutations Molecular clocks are calibrated against branches whose dates are known from the fossil record

Difficulties with Molecular Clocks The molecular clock does not run as smoothly as neutral theory predicts Irregularities result from natural selection in which some DNA changes are favored over others Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty The use of multiple genes may improve estimates

Applying a Molecular Clock: The Origin of HIV Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

Fig Year Index of base changes between HIV sequences Range Computer model of HIV