Week 3 Lecture Notes
“Can evolution be speeded up [over what was proposed by Darwin & the Synthetic “Theory”]?
∙ Apparently it can be: One model that emerged from this question was the Eldredge-Gould Punctuated Equilibrium Model
o Punctuated equilibrium (also called punctuated equilibria) is a theory in evolutionary biology which proposes that once species appear in the fossil record they will become stable, showing little net evolutionary change for most of their geological history. This state is called stasis.
o Fossil species often show long periods of no change (“stasis” = equilibrium) that were punctuated by what seemed to be rapid evolution that transformed one species into another.
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∙ Anagenesis – graduate change in a “paleospecies” in response to environmental changes – a single species (lineage) is involved
∙ The Punctuated Equilibrium model proposes discontinuous, rapid evolution of new species.
∙ Definition of microevolutionary processes: evolution at the population level.
∙ Gene versus allele: An allele is a form of a single specific type of gene.
∙ For purposes of this evolution class, this convention will be used:
o For gene A, the alleles will be: a1, a2, a3, … etc.
o The various genotypes (genotypic combinations of A’s alleles) will be: a1a1, a1a2, a1a3, a2a2, a2a3, a3a3, etc. If you want to learn more check out Is a salary better than a wage?
o For gene B, the alleles will be: b1, b2, etc.
o So – upper case letters for genes, lower case letters with subscripts to indicate individual alleles for that gene Don't forget about the age old question of How can you tell the difference between sporophyte and gametophyte?
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o There is no indication of the type of “dominance” present in this notation
∙ Punnett Square
o Diagram that is used to predict an outcome of a particular cross or breeding
o It is named after Reginald C. Punnett, who devised the approach
▪ 20 June 1875 – 3 January 1967
▪ British geneticist
▪ Co-founded the Journal of Genetics in 1910 with William Bateson
▪ Mendelism (1905) is sometimes said to have been the first textbook on
o The diagram is used by biologists to determine the probability of an offspring having a particular genotype
o The Punnett square is a tabular summary of possible combinations of
maternal alleles with paternal alleles
o These tables can be used to examine the genotypic outcome probabilities of the offspring of a single trait (allele), or when crossing multiple traits from the parents o The Punnett Square is a visual representation of Mendelian inheritance.
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Dominance and recessivity
∙ Phenotype: what is expressed by a genotype
∙ Genotype: actual allelic composition that an individual possesses for a gene
o Recessive alleles are not expressed in the heterozygous condition.
o The phenomenon of dominance, when it occurs, is a general adaptation.
∙ Complete dominance: The phenotype of the heterozygous genotype is identical to the dominant homozygous genotype. If you want to learn more check out What are the five different classifications of d curves?
∙ Complete recessivity: The phenotype of the heterozygous genotype shows no traces of the phenotype of the homozygous recessive.
∙ Semidominance (aka Incomplete Dominance): There is a “dosage effect” to possessing an allele so that the heterozygous phenotype is intermediate between either homozygous phenotypes. o Example in carnations, there is a red flower phenotype caused by a homozygous dominant allele, and a white flower phenotype caused by a recessive homozygous genotype. The heterozygous offspring are pink. If the pink carnation plants are crossed (interbred), the offspring will be ¼ red, ½ pink, and ¼ white.
∙ Codominance: Each allele is expressed at is full value in the heterozygous condition. This type of dominance is probably very common in nature.
o Usual example: ABO blood group in human beings
Other miscellaneous genetic phenomena:
∙ Epistasis: the expression of one gene (in the phenotype) will be affected by the expression of a second gene.
∙ Polygenic traits: genotypes that result in phenothypes that are governed by more than one gene (classic example, height in human beings)
∙ Penetrance: variation in the degree of phenotypic expression. E.g., polydactyly in human beings, governed by a dominant allele, has incomplete penetrance.
∙ Where do alleles come from?
o The mutations that concern us here are those that occur in the gametes (or progenitor cells of gametes) prior to fertilization and zygote formation in sexually reproducing multicellular organisms.
o Mutations that occur in the non-gametes, the somatic cells, (in sexually reproducing organisms) have little effect on evolutionary processes.
o In asexually reproducing multicellular organisms, mutation in somatic cells may have such an effect (but it is unlikely).
o In asexually reproducing unicellular organisms (e.g., amoeba), all mutations are very important.
o Also, there can be evolutionarily important mutations in other sorts of propagules produced by meiosis (e.g, spores).
∙ Mutations can be induced experimentally or accidentally by exposure to “mutagens.” But these are usually not important as an evolutionary factor in wild populations.
∙ Technically, all genes are subject to mutation. It is a spontaneous process independent of natural selection and independent of the mutations effect on fitness.
∙ Every gene will have a mutation rate (µ), and the rate will be different for every gene. Even within a gene, there may be different mutation rates for different alleles.
∙ So a1 may mutate to a2 at one rate, but the back mutation rate from a2 back to a1 may well be different. ∙ Mutation rates are not large numbers
o a high mutation rate would be 10-6 mutations per genetic locus per generation. o A very low rate would be 10-11 mutations per locus per generation. (Locus = location of a gene on a chromosome).
∙ Mutation rates are inversely related to the size of the genome – the smaller the genome size, the greater the observed rate of mutations.
∙ Mutations specifically alter the production of macromolecules. Some macromolecules are very sensitive to mutations, and the slightest alteration in them result in a non-functional molecule (and a dead gamete). Other macromolecules can withstand considerable mutations and still keep functioning normally
Types of Mutations:
∙ Substitutions in the genetic code: These are one type of “point mutations” that may be selectively neutral in many cases (Kimura’s neutrality hypothesis).
o Or they will have very slight phenotypic effects. A point mutation involves only a single nucleotide.
o Substitutional changes that cause no change to the code-specified amino acid are called synonymous or silent mutations.
o These occur especially frequently in the third codon position because of the
“redundancy” of the genetic code.
o There are other considerations, such that substitution of an “A” for “T” occurs 10% more frequently than an A to a C or an A to a G.
∙ However, a substitution that results in a “stop codon” being formed may well be a lethal mutation because in terminates transcription of the amino acid.
o A substitution that results in a different amino acid being placed in the sequence may or may not have an effect on the biomolecule produced – it can be acted upon by natural selection for good or ill.
∙ Effects of substitutions can be anything from complete lethality to complete neutrality for a gamete. o If the biomolecule being formed has a high tolerance for nucleotide substitutions, then a large mutation rate for that mutation will be detected.
o Intolerance results in detection of a slow mutation rate.
∙ Mutations that are lethal to gametes will go undetected because they will be included in no surviving zygotes and offspring
∙ All macromolecules will accumulate neutral mutations at the nucleotide level over time. Therefore, the nucleotide sequence that is present in any of genes right now will be different in those of your descendants 1000 years from now.
∙ Different molecules may well have different rates.
o Example the rate of mutation in hemoglobin is less than the rate of some
fibrinopeptides, and greater than the rate of cytochrome C
∙ The rate of evolution in each type of biomolecule, however, seems more or less constant across all diploid organisms that have inherited the original nucleotide sequence from a common ancestor (we call these homologous sequences (specifically, orthologous sequences).
o The homologous may be used correctly in biology only three ways: a) for homologous chromosomes, b) for homologous antigens, and c) for attributes of organisms
(including nucleotide sequences) that are inherited from a common ancestor.
o In all of these, the word applies to an either-or condition, and is never an expression of relative similarity.
∙ These observations about the rate of evolution have fueled a concept called the “molecular clock.” o The “clock” is based on the observance of differences between nucleotide sequences (or differences in amino acid sequences) for homologous proteins in evolutionarily divergent species of organisms that share a common ancestral species.
o One can infer how long these species have been diverged (separated) as distinct from each other (that is, their ancestral species).
o Human beings versus chimpanzees, gorillas, orangutans, other primates can be compared biomolecule by biomolecule. Or animals and fungi can be compared.
∙ Calibration of the ‘clock’ is heavily dependent on inferences made from the fossil record of organisms.
Other Types of Mutations
∙ Deletions and insertions: These cause the notorious frame-shift mutations that usually have a dramatic impact on the amino acid chains that derived from a nucleotide sequence. They may be point mutations (involve a single nucleotide), or may consist of sequences that are thousands of nucleotides long. Effects of major mutations like these are often only detected when they involve regulatory genes.
∙ Inversions – Reversal of the nucleotide sequence (entire gene on the chromosome). ∙ Translocations – moving pieces of chromosomes or entire genes from one chromosome to another. ∙ Duplication – mutations that duplicate an entire gene – an extra copy is produced.
o These can have evolutionary consequences – The duplicated gene basically is a back-up copy of the original of the gene in the gamete.
o That back-up may accumulate non-neutral mutations at a greater rate than the original.
o There are several instances where gene duplications have apparently occurred in various lineages of organisms.
o Example: Lactate Dehydrogenase A and B. LDH-A and LDH-B are present in all vertebrate animals, and are the result of an ancient gene duplication. There was a third gene duplication in LDH that occurred in derived fishes (teleosts), LDH-C. LDH-A in a species is orthologous LDH-A in another species. LDH-A in an organism is paralogous (not truly homologous) to LDH-B in another organism.
∙ Robertsonian mutations. A general type of chromosomal mutation, the most frequently cited as being important to evolution of populations are centromeric fusions and centromeric fissions. These mutations affect the diploid number in gametes.
Robertsonian Mutations Diagram
∙ The Robertsonian mutations are detected by the study of the morphology of chromosomes as they appear during their most condensed state during Metaphase. Often karyotypes are used for these studies. A karyotype is an image of the chromosome complement of a diploid organism’s cells when the chromosomes are most condensed.
Examples of karyotypes from lizards
∙ In the above lizard species, there are three pairs of large, X-shaped (“bi-armed”) somatic chromosomes in this karyotype. Compare with this next karyotype from a different species:
∙ In this species, only one large X-shaped somatic chromosome is present
∙ Robertsonian centromeric fissions to Xshaped chromosmes (pair 2 and pair 3 in the previous species) have produced to new sets of V-shaped chromosomes in this second species.
Other Types of Chromosomal Mutations
∙ Aneuploidy: A second type of whole-chromosome mutation.
o Aneuploidy results from the failure of one of the chromosomes to segregate properly during Meiosis I – such that one of the daughter cells has an extra chromosome, and the other daughter cell has one too few chromosomes (and dies).
o If this n+1 gamete is fertilized by a normal haploid gamete, then a 2n+1zygote will form.
o Even if the aneuploidy zygote survives, it will develop into an organism (plant or animal) with reduced fitness.
∙ Polyploidy: an extreme case of meiotic failure, where all of the chromosomes go into one daughter cell at Meiosis I, and the other cell gets no chromosomes.
o This phenomenon is called complete non-disjunction of chromosomes.
o The resultant gamete will be diploid (2n), not haploid.If the diploid gamete is fertilized by a normal haploid gamete, the zygote will have three sets of chromosomes, a
condition called triploid (3n).
o Triploid zygotes that survive (and many will) will usually be sterile as adult – because the sets of chromosomes interact poorly when the adult triploid tries to use meiosis to produce its gametes.
o Triploids have reduced fitness (and most are sterile, if they are sexually reproducing species).
∙ “The paradoxical nature of mutations”
∙ Some mutations are lethal to those that possess them – these can be difficult to detect if they kill the gametes or the zygotes in the early stages of development.
∙ Most mutations seem to be “bad” (the official term is deleterious) in a particular environment. ∙ But, since mutation is the ultimate source of variation in populations, they cannot always be deleterious in every environment.
∙ Many detectable mutations produce recessive alleles, so that potentially deleterious alleles, and potentially favorable alleles, are masked by the phenotype of the dominant allele on the other homologous chromosome.
∙ The appearance of a mutation upon which selection can act (that is a non-neutral mutation) is not teleological.
∙ There is no such thing as “directed mutation” in nature. Some aspects of mutation are non-random o Example: the point mutation from A to T being more frequent than the others ∙ However, appearance of a favorable mutation or an unfavorable mutation at the individual level within a population is apparently completely random.
∙ Therefore, there can be no “selective pressure” for a favorable allele to appear in a population – no matter how much the population might “benefit” from having it appear.
∙ Selection can favor a mutation only when it is expressed in an individual’s phenotype