The Origins of Genetic Variation

The Origins of Genetic Variation Lecture 2-3

Lecture Ideas • Genetic variation is a necessary condition for evolution • Variability is achieved through the process of mutation: • Mutation rate (per individual gene per generation) is low but provides abundant genetic variation within a population • Mutation is NOT the cause of evolution

Lecture Outline • Gene Structure • Gene Mutations • Definition • Types • Point mutations • Mutations arising from recombination • Mutations arising from transposable elements • Mutation Rates • Mutation effects: phenotype and fitness • Chromosome Changes • Types

The Origins of Genetic Variation Feb 2001 Publications of the complete sequence of the human genome Since then Publication of the complete sequence of more than a hundred species genome Comparison among these sequences will provide information about the processes and history of evolution To understand how the differences among sequences arose, and how phenotypic differences among organisms evolved, we must begin with the process of mutation Each of us was born with at least 300 new mutations. These mutations can be harmful, neutral, or beneficial. Here we will discuss the bright side of mutation Mutation is not the cause of evolution but it is the necessary, although not sufficient, condition for evolution.

Genes and Genomes Organisms’ genomes consist of DNA (except in certain viruses in which it is RNA) • DNA: Made up of nucleotide base pairs (bp) • Base pairs consist of: • a purine: adenine or guanine • a pyrimidine: thymine or cytosine GENE: Portion of a chromosome’s DNA that is transcribed into RNA These RNAs may or may not be translated into proteins Locus: Chromosome site occupied by a particular gene

Genes and Genomes One strand of a protein-encoding gene is transcribed into RNA In eukaryotes, the transcribed sequence of a gene consists of coding regions (Exons) separated by non-coding regions (Introns) After a gene is transcribed, the portions transcribed from exons are processed into a messenger RNA by splicing out the portions that were transcribed from introns Control Regions: Untranscribed sequences (Enhancers and Repressors) to which regulatory proteins produced by other genes bind and regulate transcription of a gene Alternative Splicing: the mature mRNA may correspond to different combinations of exons and can result in several proteins being encoded by a single gene

Genes and Genomes Through the action of ribosomes, enzymes and tRNAs, messenger RNA is translated into a polypeptide or protein on the basis of the Genetic Code CodonTriplet of bases that specifies a particular amino acid in the growing polypeptide chain The genetic code, consists of 64 codon which encode 20 amino acids Most of the amino acids are encoded by two or more synonymous codons • The third position in the codon is the most degenerate. The second position is least degenerate • A substitution of one base for another in the third position usually does not result in an amino acid substitution in a protein Three of the 64 codons are stop signals that terminate translation The genetic code is nearly universal from viruses and bacteria to pineapples and mammals. The machinery of transcription and translation is remarkably uniform.

Genes and Genomes In eukaryotes the vast majority of DNA has no apparent function Only 28% of the human genome is thought to be transcribed, and much of this consists of introns, so less than 5% of the genome encodes proteins At least 45% of the human genome consists of repeated sequences: • Tandem Repeats (including microsattelites) <100 bp • Short Interspersed Repeats (SINEs) of 100-400bp Capable of undergoing or have been formed by the process of transposition • Long Interspersed Repeats (LINEs) >5 kb • DNA Transposons Transposition: The production of copies that become inserted into new positions in the genome Transposable Elements: DNA sequences that are capable of transposition

Genes and Genomes Many protein-encoding genes (at least 40% of human genes) are members of gene families Gene Families: Groups of genes that are similar in sequence and often have related functions Example: Human hemoglobin gene family encompass two subfamilies (blue and green ) PSEUDOGENES: Sequences that resemble the functional genes, but which differ at a number of base pair sites and are not transcribed because they have internal “stop” codons Example: Human hemoglobin gene family include hemoglobin pseudogenes (black)

Gene Mutations • Mutation Refers to: • The process of alteration of a gene or chromosome • The altered state of a gene or chromosome • in Practice • The alteration of a gene from one form (or allele) to another, the alleles being distinguished by phenotypic effects • in Molecular Context • The alteration of a DNA sequence independent of whether or not it has a phenotypic effect Haplotype A particular DNA sequence that differs by one or more mutations from homologous sequences Genetic Markers Detectable mutations that geneticists use to recognize specific regions of chromosomes or genes

Gene Mutations Mutations have evolutionary consequences only if they are transmitted to succeeding generations Mutations in somatic cells are not transmitted in organisms in which the germ line is segregated from the soma early in development Mutations occur mostly during DNA replication which usually occurs during cell division Most changes are repaired by DNA polymerase and by proof reading enzymes but some are not A particular mutation occurs in a single cell of a single individual organism If because of natural selection or genetic drift it becomes fixed (i.e. is carried by nearly the entire population), the mutation may be referred to as a substitution Most mutations do not become substitutions, consequently, mutation is not equivalent to evolution

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Gene Mutations Kinds of Mutations POINT MUTATION Mutation that maps to a single gene locus This term is often restricted to single BASE PAIR SUBSTITUTIONS: • TRANSITION • Purine for purine A <-> G • Pyrimidine for pyrimidine C <-> T • TRANSVERSION • Purine for pyrimidine A, G -> C, T • Pyrimidine for purine C, T -> A, G

Gene Mutations Kinds of Mutations Mutations may have a phenotypic effect only if they occur in genes that encode ribosomal and transfer RNA, non-translated regulatory sequences such as enhancers or protein-coding regions SYNONYMOUS MUTATIONS: Mutations that have no effect on the amino acid sequence of the polypeptide or protein NON-SYNONYMOUS MUTATIONS: Mutations that result in amino acid substitutions. They may have little or no effect on the phenotype or they may have substantial effects

Gene Mutations Kinds of Mutations If a single base pair becomes inserted into or deleted from a DNA sequence, the triplet reading frame is shifted by one nucleotide, so that downstream triplets are read as different codons and translated into different amino acids Such insertions or deletions result in Frameshift Mutations

Gene Mutations Kinds of Mutations Sequence Changes Arising from Recombination When homologous DNA sequences differ at two or more base pairs, Intragenic Recombination between them can generate new DNA sequences, just as crossing over between genes generates new gene combinations

Gene Mutations Kinds of Mutations Gene Conversion Refers to cases in which during recombination one of the two alleles of a heterozygote is replaced by (converted to) the other allele

Gene Mutations Kinds of Mutations UNEQUAL CROSSING OVER can occur between two homologous sequences or chromosomes that are not perfectly aligned Normal Pairing ABBC ABBC Mispairing ABBC ABBC Unequal crossing over AB BC A BBC Products ABBBC Tandem Duplication ABC Deletion

Gene Mutations Kinds of Mutations Changes Caused by Transposable Elements Most transposable elements produce copies that can move to any of many places in the genome, and sometimes they carry with them other neighboring genes These DNA sequences include genes that encode enzymes that accomplish the transposition (movement) • The kinds of TEs include: • INSERTION SEQUENCES • Encode enzymes that cause transposition • TRANSPOSONS • Encode enzymes that cause transposition and other functional genes as well

Gene Mutations Kinds of Mutations • Retroelements • Carry a gene for the enzyme reverse transcriptase • First transcribed into RNA, then reverse transcribed into a DNA copy that is inserted

Gene Mutations Kinds of Mutations Changes Caused by Transposable Elements • Transposable elements are known to have many effects on genomes: • When inserted into a coding region they alter the function of the protein (frameshift or altering splicing patterns) • When inserted into control regions they alter gene expression • Increase mutation rates of host genes

Gene Mutations Kinds of Mutations • Cause rearrangements in the host genome resulting from recombination between two copies of a TE located at different sites • Recombination between two copies of a TE with the same sequence polarity DELETES the region between them • Recombination between two copies of a TE with the opposite sequence polarity INVERTS the region between them

Gene Mutations Kinds of Mutations • Retroelements insert DNA copies not only of their own RNA but also of RNA transcripts of other genes into the genome. These retrosequences resemble the exons of ancestral gene located elsewhere in the genome but they lack control regions and introns. Most retrosequences are processed pseudogenes which do not produce functional gene products • By transposition and unequal crossing over TEs can increase in number and so increase the size of the genome

Gene Mutations Rates of Mutation • The rate at which a particular mutation occurs is typically measured in terms of the number of independent origins per gene copy per generation • Estimating Mutation Rates • Direct Method • Count the number of mutations arising in a laboratory stock scoring mutations either by their phenotypic effects or by molecular methods • The average mutation rate measured by phenotypic effects has been estimated at 10-5 to 10-6 mutations per gamete per generation

Gene Mutations Rates of Mutation • Indirect Method • Count the number of base pair differences between homologous genes in different species relative to the number of generations that have elapsed since they diverged from their common ancestor • The average mutation rate per base pair has been estimated at 10-10 to 10-11 per replication in prokaryotes or 10-9 per sexual generation in eukaryotes

Gene Mutations Rates of Mutation • Evolutionary Implications • With such a low mutation rate per locus it might seem that mutations occur so rarely that they cannot be important. However, summed over all genes, the input of variation by mutation is considerable Mutation rate: 2.5x10-8 per bp, ind, gen Human genome: 7x109 bp 2.5x10-8 x 7x109=175 new mutations per ind per gen 2.5% genome is transcribed 175 x 0.025=4.3 mutations per ind per gen can affect phenotype 300 million people in the USA 1.29 billion mutations under natural selection only in the USA

Gene Mutations Rates of Mutation • Mutation rates vary among genes and chromosome regions and they are also affected by environmental factors (MUTAGENS) • Mutation rates in mice estimated from DNA sequences of 2 loci in their offspring. The mice were placed for 10 weeks in rural and industrial sites where they were exposed either directly to the air or to air passed through a filter

Gene Mutations Rates of Mutation • Mutation alone does not cause a character to evolve from one state to another because its rate is too slow

Gene Mutations Phenotypic Effects of Mutations • A mutation may alter one or more phenotypic characters, such as size, coloration, or the amount of activity of an enzyme. Alterations in such features may affect survival and/or reproduction, the major components of FITNESS. • The phenotypic effects of mutational changes in DNA sequence range from none to drastic.

Gene Mutations Phenotypic Effects of Mutations • Mutations induced by insertion of transposable elements in Drosophila alters the number of abdominal bristles • Homeotic mutations in Drosophila redirect the development of one body segment into that of another • Mutations in the Antennapedia gene complex, for example, cause legs to develop in place of antennae

Gene Mutations Phenotypic Effects of Mutations • Dominance describes the effect of an allele on a phenotypic character when it is paired with another allele in the heterozygous condition. • A fully dominant allele A1 produces nearly the same phenotype when heterozygous A1A2 as when homozygous A1A1. Its partner allele A2 in that instance is fully recessive • Inheritance is said to be additive if the heterozygote’s phenotype is precisely intermediate between those of the homozygote

Gene Mutations Effects of Mutations on Fitness • The effects of new mutations may range from: • Highly Advantageous • Neutral • Highly Disadvantageous • The average, or net, effect of those that do affect fitness is deleterious • The fitness consequences of many mutations depend on the population’s environment • Most mutations are Pleiotropic (they affect more than one character) • Example: • Yellow mutation in Drosophila affects not only body color, but also several components of male courtship behavior

Gene Mutations Effects of Mutations on Fitness • Evolution would not occur unless some mutations were advantageous • Fitness of a bacterial genotype is defined as its rate of increase in numbers relative to that of another genotype with which it competes in the same culture Cooper and Lenski 2000 • This method was used to trace the increase of fitness in populations of E. coli for 20,000 generations • Each population was initiated with a single individual and was therefore genetically uniform at the start • Fitness increased substantially (rapidly at first but at a decelerating rate later)

Mutation as a Random Process • Mutations occur at random: • It does not mean • All conceivable mutations are equally likely to occur due to developmental constraints • All loci are equally mutable for geneticists have described differences in mutation rates • Environmental factors cannot influence mutation rates • It does mean • The spontaneous process of mutation is stochastic • Although we may be able to predict the probability that a certain mutation will occur we cannot predict which of a large number of gene copies will undergo the mutation • The environment does not induce adaptive mutations • Mutation is random in the sense that the chance that a particular mutation will occur is not influenced by whether or not the organism is in an environment in which that mutation would be advantageous

Mutation as a Random Process • The argument that adaptively directed mutation does not occur is one of the fundamental tenets of modern evolutionary theory • Method of replica plating used to show that mutations for penicillin resistance arise spontaneously before exposure to penicillin rather than being induced by that exposure

Lynch M Mol Biol Evol 2006;23:450-468

Recombination and Variation • All genetic variation owes its origin ultimately to mutation, but in the short term, a great deal of genetic variation within a populations arises through recombination • In sexually reproducing eukaryotes, genetic variation arises from two processes: Union of genetically different gametes {A1B1} {C1D1} {A1B1} {C1D1} X {A2B2} {C2D2} {A2B2} {C2D2} Formation of gametes with different combinations of alleles Crossing over between homologous chromosomes Independent segregation of non-homologous chromosomes {A1B1} {CiDj} {A1B1} {C1D1} {A1B2} {CiDj} {A1B1} {C2D2} {A1 B1} {C1D1} {A1B1} {C1D1} X X {A2 B2} {C2D2} {A2B2} {C2D2} {A2B1} {CiDj} {A2B2} {C1D1} {A2B2} {CiDj} {A2B2} {C2D2}

Lynch M Mol Biol Evol 2006;23:450-468

Recombination and Variation • Recombination can both increase and decrease genetic variation • In sexually reproducing populations, genes are transmitted to the next generation but genotypes are not: they end with organisms’ deaths, and are reassembled anew in each generation • Recombination, therefore has complicated effects on variation: • Retards adaptation by breaking down favorable gene combinations • Enhances adaptation by providing natural selection with different combinations of alleles that have arisen by mutation

Alterations of the Karyotype • KARYOTYPE Description of an organism’s complement of chromosomes (number, size, shape, internal arrangement) • Aneuploidy Situation in which the chromosome content within a given cell is abnormal. For example in a diploid organism having 1 or 3 copies of a chromosome • Chromosome structure may be altered by: • Duplications • Deletions • Polyploidy • Rearrangements of one or more chromosomes

Alterations of the Karyotype Polyploidy • Diploid organism has two entire sets of homologous chromosomes (2N); a polyploid organism has more than two • Polyploids can be formed when failure of the reduction division in meiosis produces diploid gametes • The union of an unreduced gamete (2N) and a reduced gamete (N) yields a triploid (3N) zygote

Alterations of the Karyotype Chromosome Rearrangements • Changes in the structure of chromosomes constitute another class of karyotipic alterations • These changes are caused by breaks in chromosomes followed by rejoining of pieces in new configurations • Some such changes can affect the pattern of segregation in meiosis, and therefore affect the proportion of viable gametes • Individual organisms may be homozygous or heterozygous for a rearranged chromosome, and are sometimes referred to as homokaryotypes or heterokaryotypes respectively

Alterations of the Karyotype Chromosome Rearrangements Inversions • Consider a segment of a chromosome in which ABCDE denotes a sequence of genes. If a loop is formed, and breakage and reunion occur at the point of overlap, a new sequence , such as ADCBE, may be formed • An inversion can be: • PERICENTRIC If it includes the centromere • PARACENTRIC If it does not include the centromere

Alterations of the Karyotype Chromosome Rearrangements • Alignment of the genes on the normal and inverted chromosomes requires the formation of a loop • Assume that in a paracentric inversion, crossing over occurs between loci such as B and C

Alterations of the Karyotype Chromosome Rearrangements • One strand lacks certain gene regions and also lacks a centromere: It will not migrate to either pole, and is lost • The other strand not only lacks some genetic material, but also has two centromeres, so the chromosome breaks when these centromeres are pulled to the opposite poles: the resulting daughter cells lack certain gene regions and will not form viable gametes • When inversion takes place, fertility is reduced because many gametes are inviable, and recombination is effectively suppressed because gametes carrying the recombinant chromosomes, which lack some genetic material are inviable

Alterations of the Karyotype Chromosome Rearrangements Translocations • By breakage and reunion two nonhomologous chromosomes may exchange segments resulting in a reciprocal translocation • Meiosis in translocation heterokaryotype often results in a high proportion of aneuploid gametes, so the fertility of translocation heterokaryotypes is often reduced by 50 per cent or more

The Origins of Genetic Variation