Molecular Level of Genetics
Most of the molecules found in humans and other living organisms fall into one of four categories:

1. carbohydrates (sugars and starches) 2. lipids (fats, oils, and waxes)
3. proteins
4. nucleic acids

Proteins are large chain-like molecules that are twisted and folded back on themselves in complex patterns. They serve as structural material for the body, gas transporters, hormones , antibodies , neurotransmitters , and enzymes . In fact, when looking at someone, you mostly see proteins since skin and hair are primarily made of them. Proteins acting as enzymes are particularly important substances because they trigger and control the chemical reactions by which carbohydrates, lipids, and other substances are created. When you look at another human being, you mostly see proteins.

Our bodies produce about 90,000 thousand different kinds of proteins, all of which consist of sim- pler units called amino acids .

Proteins in all organisms are mostly composed of just 20 kinds of amino acids. Proteins differ in the number, sequence, and kinds of amino acids. Our bodies produce some of these amino acids, while others come directly from food that we consume.

AMINO ACIDS

Proteins, and subsequently amino acids, are mostly made up of just four elements: carbon, oxygen, hydrogen, and nitrogen. In fact, 96.3% of your body is composed of these common elements.

The largest molecules in people and other organisms are nucleic acids. Like proteins, they consist of very long chains of simpler units. However, the components, shapes, and functions of nucleic acids differ significantly from those of proteins. There are two basic varieties of nucleic acids: DNA (deoxyribonucleic acid ) and RNA (ribonucleic acid ). Both play critical roles in the produc- tion of proteins.

A chromosome consists mainly of one or more very long DNA molecules. Each of these molecules contains the genetic codes, or genes, for the synthesis of many different proteins and for the regula- tion of other genes. In a sense, a DNA molecule is a linear sequence of permanently stored blue- prints or recipes that are used regularly by our cells to make proteins out of amino acids.

1

3

These new identical messenger RNA molecules then leave the nucleus and go out into the cytoplasm where the protein they are coded for is actually synthesized or assembled.

mRNA migrating out of the cell nucleus

Specifically, the messenger RNA molecules migrate from the chromosomes to the ribosomes, which are small graules in the cytoplasm. Some ribosome are on the surface of mem- brane networks called endoplasmic reticula , while others are free ribosomes. Assembly of proteins takes place at the site of the ribosomes

DNA copied

mRNA migrates to cytoplasm

Generalized animal cell

Protein synthesis begins as ribosomes move along the messenger RNA strand and attach transfer RNA (tRNA) anticodons (each with 3 bases) to triplets of complementary bases on the mRNA.

protein molecule forming

Protein synthesis at the ribosomes initiated by mRNA momentarily bonding with tRNA (Note: this schematic representation is a simplification of the actual process.)

Each transfer RNA attracts and brings a specific amino acid along with it. As a ribosome translates the messenger RNA code, a protein is assembled lineally, one amino acid at a

chromosomes ribosomes

(small dots)

endoplasmic reticula

4

Not all codons specify amino acid components to be included in a protein. For instance, a start codon appears in DNA at thebeginning of the lineal code sequence for each gene and a stop codon is at the end. In other words, they indicate where a protein recipe begins and ends.

Most plant and animal cells have tens of thousands of ribosomes. Many ribosomes simultaneously translate identical strands of messenger RNA. As a result, the synthesis of proteins can be rapid and massive. These same processes can occur at the same time in millions of cells when a particu- lar protein is needed.

In addition to keeping the blueprints for protein synthesis, DNA has one further function–it replicates, or duplicates, itself. At the beginning of this process, the parent DNA molecule unwinds and unzips along its bases beginning at one end. Then in response to an enzyme, free nucleotides pair up with cor- responding bases on both of the DNA strands, as illustrated below. This results in the formation of two exact copies of the original molecule. Nuclear DNA replication occurs just before mitosis and meiosis.

DNA replication

Occasionally, an error is made in DNA replication. For example, an incorrect base pair may be included. This constitutes a mutation. If it occurs in the formation of sex cells, the mutation may be inherited and passed on in future generations. Such errors in replication are the ultimate sources of all new genes and are essential for the evolution of new species. They are also responsible for changes in somatic cells that result in the uncontrolled tumorgrowths of cancer.

It is important to realize that the genetic code system of humans is not unique but is shared by all living things. The same codons code for the same amino acids in people, dogs, fleas, and even bac- teria. In addition, we share many genes with other creatures. For instance, about 90% of human genes are identical to those of a mouse. Even more surprising is the fact that more than 1/3 of our genes are shared with a primitive group of worm species known as nematodes. The universal nature of the genetic code is compelling evidence for the evolution of all organisms from the same early life forms.

©1998, 2000 by Dennis O’Neil. Used by permission of the author.

Biology 11 Ms. Jamieson

Questions

1) Write the meanings of the following terms:

a) Adaptation

b) Evolution

c) Population

d) Fossil

e) Species

2) Why is evolution such an important scientific concept?

Name: _________________________ Date: __________ Block: _____

Chapter 2 – Adaptation and Change Read pages 60 – 67, and answer the following questions:

Examples to illustrate your answers

Information from text

an inherited trait or set of traits that improve the chancs of survival and reproduction of oranisms

the process by which populations of living things change over a series of generations

a group of individuals of the same species occupying a given area at a certain time

a group of organisms that look alike and that can interbreed under natural conditions to producce fertile offspring

3) How are fossils formed?

4) What is the geological time scale?

5) What is the Burgess Shale, and where is it?

6) How old are the fossils in the Burgess Shale, and what period in the Earth’s history do they belong to? (see Fig. 2.6 page 64)

7) Why is the Burgess Shale so important?

8) How is the Burgess Shale evidence of divergent evolution

Biology 11 Outline Notes

Classification of Organisms

Overview
Phylogeny and Systematics

• Evolutionary biology is about both process and history.
  • °  The processes of evolution are natural selection and other mechanisms that change the genetic composition of populations and can lead to the evolution of new species.
  • °  A major goal of evolutionary biology is to reconstruct the history of life on earth.
• In this chapter, we will consider how scientists trace phylogeny, the evolutionary history of a group of organisms.
• To reconstruct phylogeny, scientists use systematics, an analytical approach to understanding the diversity and relationships of living and extinct organisms.
  • °  Evidence used to reconstruct phylogenies can be obtained from the fossil record and from morphological and biochemical similarities between organisms.
  • °  In recent decades, systematists have gained a powerful new tool in molecular systematics, which uses comparisons of nucleotide sequences in DNA and RNA to help identify evolutionary relationships between individual genes or even entire genomes.
• Scientists are working to construct a universal tree of life, which will be refined as the database of DNA and RNA sequences grows.

  A. Phylogenies Are Based on Common Ancestries

  1. Sedimentary rocks are the richest source of fossils.

• Fossils are the preserved remnants or impressions left by organisms that lived in the past.
• In essence, they are the historical documents of biology.
• Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and swamps, where the minerals settle to the bottom along with the remains of organisms.
  • °  As deposits pile up, they compress older sediments below them into layers called strata.
  • °  The fossil record is the ordered array in which fossils appear within sedimentary rock strata.

     These rocks record the passing of geological time.

  • °  Fossils can be used to construct phylogenies only if we

    can determine their ages.

  • °  The fossil record is a substantial, but incomplete, chronicle of evolutionary change.

See Chapter 17

Notes

Review: Genetics
Read text chp 10 “DNA, RNA, and

Protein Synthesis.” This content is also required for Biology 12.

Conserved Sequences

are similar or identical sequences that may occur within nucleic acids (e.g., DNA), proteins or polymeric carbohydrates within multiple species of organism or within different molecules produced by the same organism. In the case of cross species conservation, this indicates that a particular sequence may have been maintained by evolution despite speciation. The further back up the phylogenetic tree a particular conserved sequence may occur the more highly conserved it is said to be.

Sequence similarities serve as evidence for structural and functional conservation, as well as of evolutionary relationships between the sequences.

Evolution: Taxonomy

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Classification of Organisms

Notes

• °  The majority of living things were not captured as fossils upon their death.

   Of those that formed fossils, later geological processes destroyed many.

   Only a fraction of existing fossils have been discovered.

• °  The fossil record is biased in favor of species that existed for a long time, were abundant and widespread, and had hard shells or skeletons that fossilized readily.

  2. Morphological and molecular similarities may provide clues to phylogeny.

• Similarities due to shared ancestry are called homologies.
• Organisms that share similar morphologies or DNA sequences are likely to be more closely related than organisms without such similarities.
• Morphological divergence between closely related species can be small or great.

° Morphological diversity may be controlled by relatively few genetic differences.

• Similarity due to convergent evolution is called analogy.
  • °  When two organisms from different evolutionary lineages experience similar environmental pressures, natural selection may result in convergent evolution.

     Similar analogous adaptations may evolve in such organisms.

  • °  Analogies are not due to shared ancestry.
• Distinguishing homology from analogy is critical in the

  reconstruction of phylogeny.

  • °  For example, both birds and bats have adaptations that allow them to fly.
  • °  However, a close examination of a bat’s wing shows a greater similarity to a cat’s forelimb that to a bird’s wing.
  • °  Fossil evidence also documents that bat and bird wings arose independently from walking forelimbs of different ancestors.
  • °  Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in function to a bird’s wing.
• Analogous structures that have evolved independently are also called homoplasies.
• In general, the more points of resemblance that two complex structures have, the less likely it is that they evolved independently.

° For example, the skulls of a human and a chimpanzee are formed by the fusion of many bones.

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Classification of Organisms

Notes

• °  The two skulls match almost perfectly, bone for bone.
• °  It is highly unlikely that such complex structures have

  separate origins.

• °  More likely, the genes involved in the development of both skulls were inherited from a common ancestor.

• The same argument applies to comparing genes, which are sequences of nucleotides.
• Systematists compare long stretches of DNA and even entire genomes to assess relationships between species.

° If genes in two organisms have closely similar nucleotide sequences, it is highly likely that the genes are homologous.

• It may be difficult to carry out molecular comparisons of nucleic acids.
  • °  The first step is to align nucleic acid sequences from the two species being studied.
  • °  In closely related species, sequences may differ at only one or a few sites.
  • °  Distantly related species may have many differences or sequences of different length.

     Over evolutionary time, insertions and deletions accumulate, altering the lengths of the gene sequences.

• Deletions or insertions may shift the remaining sequences, making it difficult to recognize closely matching nucleotide sequences.

° To deal with this, systematists use computer programs to analyze comparable DNA sequences of differing lengths and align them appropriately.

• The fact that molecules have diverged between species does not tell us how long ago their common ancestor lived.

° Molecular divergences between lineages with reasonably complete fossil records can serve as a molecular yardstick to measure the appropriate time span of various degrees of divergence.

• As with morphological characters, it is necessary to distinguish homology from analogy to determine the usefulness of molecular similarities for reconstruction of phylogenies.
  • °  Closely similar sequences are most likely homologies.
  • °  In distantly related organisms, identical bases in otherwise different sequences may simply be coincidental matches or molecular homoplasies.
• Scientists have developed mathematical tools that can distinguish “distant” homologies from coincidental matches in extremely divergent sequences.

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Classification of Organisms

Notes

° For example, such molecular analysis has provided evidence that humans share a distant common ancestor with bacteria.

• Scientists have sequenced more than 20 billion bases worth of nucleic acid data from thousands of species.

B. Phylogenetic Systematics: Connecting Classification with Evolutionary History

• In 1748, Carolus Linnaeus published Systema naturae, his classification of all plants and animals known at the time.
• Taxonomy is an ordered division of organisms into categories based on similarities and differences.
• Linneaus’s classification was not based on evolutionary relationships but simply on resemblances between organisms.

° Despite this, many features of his system remain useful in phylogenetic systematics.

1. Taxonomy employs a hierarchical system of classification.

• The Linnaean system, first formally proposed by Linnaeus in Systema naturae in the 18th century, has two main characteristics.
  • Each species has a two-part name.
  • Species are organized hierarchically into broader and

    broader groups of organisms.

• Under the binomial system, each species is assigned a two-

  part Latinized name, a binomial.

  • °  The first part, the genus, is the closest group to which a

    species belongs.

  • °  The second part, the specific epithet, refers to one

    species within each genus.

  • °  The first letter of the genus is capitalized and both names

    are italicized and Latinized.

  • °  For example, Linnaeus assigned to humans the optimistic scientific name Homo sapiens, which means “wise man.”
• A hierarchical classification groups species into increasingly broad taxonomic categories.
• Species that appear to be closely related are grouped into the same genus.

° For example, the leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris).

• Genera are grouped into progressively broader categories: family, order, class, phylum, kingdom, and domain.

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Classification of Organisms

Notes

• Each taxonomic level is more comprehensive than the previous one.

° As an example, all species of cats are mammals, but not all mammals are cats.

• The named taxonomic unit at any level is called a taxon.

° Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class level that includes all of the many orders of mammals.

• Higher classification levels are not defined by some measurable characteristic, such as the reproductive isolation that separates biological species.
• As a result, the larger categories are not comparable between lineages.

° An order of snails does not necessarily exhibit the same degree of morphological or genetic diversity as an order of mammals.

2. Classification and phylogeny are linked.

• Systematists explore phylogeny by examining various characteristics in living and fossil organisms.
• They construct branching diagrams called phylogenetic trees to depict their hypotheses about evolutionary relationships.
• The branching of the tree reflects the hierarchical classification of groups nested within more inclusive groups.
• Methods for tracing phylogeny began with Darwin, who realized the evolutionary implications of Linnaean hierarchy.
• Darwin introduced phylogenetic systematics in On the Origin of Species when he wrote: “Our classifications will come to be, as far as they can be so made, genealogies.”

  3. Phylogenetic systematics informs the construction of phylogenetic trees based on shared characters.

• Patterns of shared characteristics can be depicted in a diagram called a cladogram.
• If shared characteristics are homologous and, thus, explained by common ancestry, then the cladogram forms the basis of a phylogenetic tree.

° A clade is defined as a group of species that includes an ancestral species and all its descendents.

• The study of resemblances among clades is called cladistics. ° Each branch, or clade, can be nested within larger

clades.

• A valid clade is monophyletic, consisting of an ancestral species and all its descendents.

Evolution: Taxonomy

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Classification of Organisms

Notes

• °  When we lack information about some members of a clade, the result is a paraphyletic grouping that consists of some, but not all, of the descendents.
• °  The result may also be several polyphyletic groupings that lack a common ancestor.
• °  Such situations call for further reconstruction to uncover species that tie these groupings together into monophyletic clades.

• Determining which similarities between species are relevant to grouping the species in a clade is a challenge.
• It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.
• Systematists must also sort through homologous features, or characters, to separate shared derived characters from shared primitive characters.

  ° A “character” refers to any feature that a particular taxon possesses.

  ° A shared derived character is unique to a particular clade.

  ° A shared primitive character is found not only in the clade being analyzed, but also in older clades.

• For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.

° It is a shared derived character that uniquely identifies mammals.

• However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.

° Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.

• Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.

° The status of a character shared derived versus shared primitive may depend on the level at which the analysis is being performed.

• A key step in cladistic analysis is outgroup comparison, which is used to differentiate shared primitive characters from shared derived ones.
• To do this, we need to identify an outgroup, a species or group of species that is closely related to the species that we are studying, but known to be less closely related than any members of the study group are to each other.
• To study the relationships among an ingroup of five vertebrates (a leopard, a turtle, a salamander, a tuna, and a

Evolution: Taxonomy

6

Classification of Organisms

Notes

lamprey) on a cladogram, an animal called the lancelet is a good choice.

° The lancelet is a small member of the Phylum Chordata that lacks a backbone.

• The species making up the ingroup display a mixture of shared primitive and shared derived characters.
• In an outgroup analysis, the assumption is that any homologies shared by the ingroup and outgroup are primitive characters that were present in the common ancestor of both groups.
• Homologies present in some or all of the ingroup taxa are assumed to have evolved after the divergence of the ingroup and outgroup taxa.
• In our example, a notochord, present in lancelets and in the embryos of the ingroup, is a shared primitive character and, thus, not useful for sorting out relationships between members of the ingroup.
  • °  The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup.
  • °  The presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram.
• Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.
• A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.
  • °  However, this chronology does not indicate the time of origin of the species that we are comparing, only the groups to which they belong.
  • °  For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group.
• A cladogram is not a phylogenetic tree.

° To convert it to a phylogenetic tree, we need more information from sources such as the fossil record, which can indicate when and in which groups the characters first appeared.

• Any chronology represented by the branching pattern of a phylogenetic tree is relative (earlier versus later) rather than absolute (so many millions of years ago).
• Some kinds of tree diagrams can be used to provide more specific information about timing.

Evolution: Taxonomy

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Classification of Organisms

Notes

• In a phylogram, the length of a branch reflects the number of genetic changes that have taken place in a particular DNA or RNA sequence in a lineage.
• Even though the branches in a phylogram may have different lengths, all the different lineages that descend from a common ancestor have survived for the same number of years.
  • °  Humans and bacteria had a common ancestor that lived more than 3 billion years ago.
  • °  This ancestor was a single-celled prokaryote and was more like a modern bacterium than like a human.
  • °  Even though bacteria have apparently changed little in structure since that common ancestor, there have nonetheless been 3 billion years of evolution in both the bacterial and eukaryotic lineages.
• These equal amounts of chronological time are represented in an ultrameric tree.
• In an ultrameric tree, the branching pattern is the same as in a phylogram, but all the branches that can be traced from the common ancestor to the present are of equal lengths.
• Ultrameric trees do not contain the information about different evolutionary rates that can be found in phylograms.

° However, they draw on data from the fossil record to place certain branch points in the context of geological time.

4. The principles of maximum parsimony and maximum likelihood help systematists reconstruct phylogeny.

• As available data about DNA sequences increase, it becomes more difficult to draw the phylogenetic tree that best describes evolutionary history.

° If you are analyzing data for 50 species, there are 3 × 1076 different ways to form a tree.

• According to the principle of maximum parsimony, we look for the simplest explanation that is consistent with the facts.
  • °  In the case of a tree based on morphological characters, the most parsimonious tree is the one that requires the fewest evolutionary events to have occurred in the form of shared derived characters.
  • °  For phylograms based on DNA sequences, the most parsimonious tree requires the fewest base changes in DNA.
• The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree should reflect the most likely sequence of evolutionary events.

Parsimony

In science, parsimony is to prefer least complicated explanation for an observation. This is generally regarded as good when judging hypotheses. Ockham’s Razor also states this idea

Evolution: Taxonomy

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Classification of Organisms

Notes

° Maximum likelihood methods are designed to use as much information as possible.

• Many computer programs have been developed to search for trees that are parsimonious and likely:
  • °  “Distance” methods minimize the total of all the percentage differences among all the sequences.
  • °  More complex “character-state” methods minimize the total number of base changes or search for the most likely pattern of base changes among all the sequences.
• Although we can never be certain precisely which tree truly reflects phylogeny, if they are based on a large amount of accurate data, the various methods usually yield similar trees.

  5. Phylogenetic trees are hypotheses.

• Any phylogenetic tree represents a hypothesis about how the organisms in the tree are related.

° The best hypothesis is the one that best fits all the available data.

• A hypothesis may be modified when new evidence compels systematists to revise their trees.

° Many older phylogenetic hypotheses have been changed or rejected since the introduction of molecular methods for comparing species and tracing phylogeny.

• Often, in the absence of conflicting information, the most parsimonious tree is also the most likely.

  ° Sometimes there is compelling evidence that the best hypothesis is not the most parsimonious.

  ° Nature does not always take the simplest course.

  ° In some cases, the particular morphological or molecular character we are using to sort taxa actually did evolve multiple times.

• For example, the most parsimonious assumption would be that the four-chambered heart evolved only once in an ancestor common to birds and mammals but not to lizards, snakes, turtles, and crocodiles.
• But abundant evidence indicated that birds and mammals evolved from different reptilian ancestors.
  • °  The hearts of birds and mammals develop differently, supporting the hypothesis that they evolved independently.
  • °  The most parsimonious tree is not consistent with the above facts, and must be rejected in favor of a less parsimonious tree.
• The four-chambered hearts of birds and mammals are analogous, not homologous.

Evolution: Taxonomy

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Classification of Organisms

Notes

• Occasionally misjudging an analogous similarity in morphology or gene sequence as a shared derived homology is less likely to distort a phylogenetic tree if several derived characters define each clade in the tree.

° The strongest phylogenetic hypotheses are those supported by multiple lines of molecular and morphological evidence as well as by fossil evidence.

6. An organism’s evolutionary history is documented in its genome.

• Molecular systematics is a valuable tool for tracing an organism’s evolutionary history.
• The molecular approach helps us to understand phylogenetic relationships that cannot be measured by comparative anatomy and other nonmolecular methods.

° For example, molecular systematics helps us uncover evolutionary relationships between groups that have no grounds for morphological comparison, such as mammals and bacteria.

• Molecular systematics enables scientists to compare genetic divergence within a species.

° Molecular biology has helped to extend systematics to evolutionary relationships far above and below the species level.

• Its findings are sometimes inconclusive, as in cases where a number of taxa diverged at nearly the same time.
• The ability of molecular trees to encompass both short and long periods of time is based on the fact that different genes evolve at different rates, even in the same evolutionary lineage.

° For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively slowly, so comparisons of DNA sequences in these genes can be used to sort out relationships between taxa that diverged hundreds of millions of years ago.

• In contrast, mitochondrial DNA (mtDNA) evolved relatively recently and can be used to explore recent evolutionary events, such as relationships between groups within a species.

7. Gene duplication has provided opportunities for evolutionary change.

• Gene duplication increases the number of genes in the genome, providing opportunities for further evolutionary change.
• Gene duplication has resulted in gene families, which are groups of related genes within an organism’s genome.

Introns & Exons (grade 10 review)

Introns are sections of DNA within a gene that do not encode part of the protein that the gene produces, and are spliced out of the mRNA that is transcribed from the gene before it is exported from the cell nucleus. Introns exist mainly (but not only) in eukaryotic cells. The regions of a gene that remain in the spliced mRNA are called exons.

Source: Wikipedia

Introns = interruptions in the DNA Exons = expressed DNA code

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Classification of Organisms

Notes

• Like homologous genes in different species, these duplicated genes have a common genetic ancestor.
• There are two types of homologous genes: orthologous genes and paralogous genes.
• The term orthologous refers to homologous genes that are found in different gene pools because of speciation.

° The ß hemoglobin genes in humans and mice are orthologous.

• Paralogous genes result from gene duplication and are found in more than one copy in the same genome.
  • °  Olfactory receptor genes have undergone many gene duplications in vertebrates.
  • °  Humans and mice each have huge families of more than 1,000 of these paralogous genes.
• Now that we have compared entire genomes of different organisms, two remarkable facts have emerged.
• Orthologous genes are widespread and can extend over enormous evolutionary distances.
  • °  Approximately 99% of the genes of humans and mice are demonstrably orthologous, and 50% of human genes are orthologous with those of yeast.
  • °  All living things share many biochemical and development pathways.
• The number of genes seems not to have increased at the same rate as phenotypic complexity.
  • °  Humans have only five times as many genes as yeast, a simple unicellular eukaryote, although we have a large, complex brain and a body that contains more than 200 different types of tissues.
  • °  Many human genes are more versatile than yeast and can carry out a wide variety of tasks in various body tissues.

    8. Molecular clocks may keep track of evolutionary time.

• In the past, the timing of evolutionary events has rested primarily on the fossil record.
• One of the goals of evolutionary biology is to understand the relationship among all living organisms, including those for which there is no fossil record.
• Molecular clocks serve as yardsticks for measuring the absolute time of evolutionary change.
  • °  They are based on the observation that some regions of the genome evolve at constant rates.
  • °  For these regions, the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the two species last shared a common ancestor.

Homologous genes – genes having similar structures and functions.

Paralogous – two genes or clusters of genes at different chromosomal locations in the same organism that have structural similarities indicating that they derived from a common ancestral gene.

Orthologous – homologous genes that originated through speciation, i.e., genes in different species, that are similar to each other because they originated from a common ancestor (for example, human and mouse, e.g., globin (transport) protein).

Source: Wikipedia

Gene Duplication

Gene duplication occurs when an error in DNA replication leads to the duplication of a region of DNA containing a (generally functional) gene. The significance of this process for evolutionary biology is that if a gene is under natural selection, most mutations will lead to the death of the organism. When a gene is duplicated selection may be removed from one copy and now the other gene locus is free to mutate and discover new functions.

The two genes that exist after a gene duplication event are called paralogs and usually code for proteins with a different function and/or structure. By contrast, orthologous genes are ones which code for proteins with similar functions but exist in different species, and are created from a speciation event.

Source: Wikipedia

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Notes

° In the case of paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated.

• We can calibrate the molecular clock of a gene by graphing the number of nucleotide differences against the timing of a series of evolutionary branch points that are known from the fossil record.
  • °  The slope of the best line through these points represents the evolution rate of that molecular clock.
  • °  This rate can be used to estimate the absolute date of evolutionary events that have no fossil record.
• No molecular clock is completely accurate.
  • °  Genes that make good molecular clocks have fairly

    smooth average rates of change.

  • °  No genes mark time with a precise tick-tock accuracy in

    the rate of base changes.

  • °  Over time there may be chance deviations above and below the average rate.
• Rates of change of various genes vary greatly.

° Some genes evolve a million times faster than others.

• The molecular clock approach assumes that much of the change in DNA sequences is due to genetic drift and is selectively neutral.
  • °  The neutral theory suggests that much evolutionary change in genes and proteins has no effect on fitness and, therefore, is not influenced by Darwinian selection.
  • °  Researchers supporting this theory point out that many new mutations are harmful and are removed quickly.
  • °  However, if most of the rest are neutral and have little or no effect on fitness, the rate of molecular change should be clocklike in their regularity.
• Differences in the rates of change of specific genes are a function of the importance of the gene.
  • °  If the exact sequence of amino acids specified by a gene is essential to survival, most mutations will be harmful and will be removed by natural selection.
  • °  If the sequence of genes is less critical, more mutations will be neutral, and mutations will accumulate more rapidly.
• Some DNA changes are favored by natural selection.

° This leads some scientists to question the accuracy and

utility of molecular clocks for timing evolution.

• Evidence suggests that almost 50% of the amino acid differences in proteins of two Drosophila species have resulted from directional natural selection.

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Classification of Organisms

Notes

• Over very long periods of time, fluctuations in the rate of accumulation of mutations due to natural selection may even out.

° Even genes with irregular clocks can mark elapsed time approximately.

• Biologists are skeptical of conclusions derived from molecular clocks that have been extrapolated to time spans beyond the calibration in the fossil record
  • °  Few fossils are older than 550 million years old.
  • °  Estimates for evolutionary divergences prior to that time may assume that molecular clocks have been constant over billions of years.
  • °  Such estimates have a high degree of uncertainty.
• The molecular clock approach has been used to date the jump of the HIV virus from related SIV viruses that infect chimpanzees and other primates to humans.
  • °  The virus has spread to humans more than once.
  • °  The multiple origins of HIV are reflected in the variety

    of strains of the virus.

• HIV-1 M is the most common HIV strain.
  • °  Investigators have calibrated the molecular clock for the virus by comparing samples of the virus collected at various times.
  • °  From their analysis, they project that the HIV-1 M strain invaded humans in the 1930s.

    9. There is a universal tree of life.

• The genetic code is universal in all forms of life.
° From this, researchers infer that all living things have a

common ancestor.

• Researchers are working to link all organisms into a universal tree of life.
• Two criteria identify regions of DNA that can be used to reconstruct the branching pattern of this tree.
  • °  The regions must be able to be sequenced.
  • °  They must have evolved slowly, so that even distantly related organisms show evidence of homologies in these regions.
• rRNA genes, coding for the RNA component of ribosomes, meet these criteria.
• Two points have emerged from this effort:

1. The tree of life consists of three great domains: Bacteria,

Archaea, and Eukarya.

° Most prokaryotes belong to Bacteria.

Evolution: Taxonomy

13

Classification of Organisms

• °  Archaea includes a diverse group of prokaryotes that inhabit many different habitats.
• °  Eukarya includes all organisms with true nuclei, including many unicellular organisms as well as the multicellular kingdoms.

2. The early history of these domains is not yet clear.

• °  Early in the history of life, there were many interchanges

  of genes between organisms in the different domains.

• °  One mechanism for these interchanges was horizontal gene transfer, in which genes are transferred from one genome to another by mechanisms such as transposable elements.
• °  Different organisms fused to produce new, hybrid organisms.
• °  It is likely that the first eukaryote arose through fusion between an ancestral bacterium and an ancestral archaean.

Horizontal gene transfer –
hinders clarification of the deepest branchings in a phylogenetic tree that depicts the origins of the three domains.

Source:
Biology 7th ed, Campbell Joan Sharp, SFU

Notes

Evolution: Taxonomy

14

Biology 11 Review Notes

Classification of Organisms Appendix See Chapter 17

Vocabulary List for Chapter 17 – Classification of Organisms

Some of these terms are used for the online Crossword review.

Evolution: Taxonomy 15

Classification of Organisms Appendix

Vocabulary List by Topic (with additional terms)

Overview

Phyogeny and Systematics  phylogeny
 systematics,
 molecular systematics,

A. Phylogenies Are Based on Common Ancestries

1. Sedimentary rocks are the richest source of fossils.

fossil record

2. Morphological and molecular similarities may provide clues to phylogeny.
 analogy.
 homoplasies.

B. Phylogenetic Systematics: Connecting Classification with Evolutionary History

1. Taxonomy employs a hierarchical system of classification.
 binomial.
 genus,

 specific epithet,
 species
 hierarchical classification
 family, order, class, phylum, kingdom,  domain.
 taxon.

2. Classification and phylogeny are linked.

Etymologies

Evolution: Taxonomy 16

Classification of Organisms Appendix

Evolution: Taxonomy 17