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Exam 1 Guide Bundle

by: Tiffany Schweda

Exam 1 Guide Bundle BIOL 3321

Tiffany Schweda

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Compilation of notes with additional information and terms
Dr. Carl S. Lieb
Study Guide
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This 28 page Study Guide was uploaded by Tiffany Schweda on Monday February 22, 2016. The Study Guide belongs to BIOL 3321 at University of Texas at El Paso taught by Dr. Carl S. Lieb in Spring 2016. Since its upload, it has received 157 views. For similar materials see Evolution in Biology at University of Texas at El Paso.


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Date Created: 02/22/16
 Evolutionary thought: the concept that species change over time has its roots buried in antiquity with the ideas of the ancient Greeks, Romans and Chinese  In the late 17th century two opposing ideas helped to influence Western Biological thinking: o Essentialism: belief that every species has essential characteristics that are unalterable, this concept was developed from medieval Aristotelian metaphysics and fit with natural theology o Development of the new anti- Aristotelian approach to modern science; grew as the Enlightenment progressed; evolutionary cosmology and the mechanical philosophy spread from the physical sciences to natural history  Sir Karl Popper o July 28, 1902- September 17, 1994 o Austrian-British philosopher and professor o Regarded as one of the greatest philosophers of science of the 20th century o Rejected the classical inductivist views on the scientific method in the favor of empirical falsification  There is always going to be some level of uncertainty even when an explanation has been provided  Inductivism: traditional model of scientific method that is attributed to Francis Bacon, who in 1620 vowed to subvert allegedly traditional thinking.  Empirical falsification: statements are called falsifiable if it is possible to conceive of an observation or an argument which negates the statement in question. o In this sense, falsify is synonymous with nullify, meaning to invalidate or "show to be false"  Paradigm shift: a fundamental change in approach or underlying assumptions. Coined by Thomas Kuhn in order to describe the nature of scientific revolutions or fundamental changes in the basic concepts and experimental practices of any given scientific discipline. Origins of Scientific Thinking  Ancient Greek philosophers helped to start what is now known as science  Natural explanations for natural events were started to be used instead of attributing everything to actions by the gods  The ancient roots of biological sciences came from two different traditions o Natural history tradition  Traces all the way back to Aristotle (384-322 BCE), an ancient Ionian philosopher  One of Greece’s most famous philosophers and writers, some of his works managed to survive through the ages. o Biomedical/physiological tradition  Traces all the way back to Hippocrates (450-377 BCE)  The origin of the Hippocratic oath in the medical field comes from Hippocrates’ philosophies  Hippocrates is considered to be the founding father of medicine o Modern biological sciences seem to be back to a separation of these two traditions although at different times in the past they were more integrated  Evolutionary ideas will come from the natural history tradition o It was in the middle of the 20th century that the science fields were divided o By the middle of the 21st century it was discovered that the individual sciences couldn’t be understood by only studying one small aspect o This is because there is a crossover in the interactions  For example: biology needs chemistry and chemistry needs biology  In the simplest of expressions evolution refers to the change in populations of organisms over time by a natural process  It would take a long time during the history of western civilization for this concept to develop  Important to the retardation of the development of evolutionary thinking was the platonic doctrine of essentialism  Plato (420-340 BCE) was another famous Greek philosopher that had a heavy impact on the development of the sciences Important Aspects of Essentialism 1. Organisms don’t change over time 2. Variations seen within species of organisms is philosophically meaningless  The key thought is that everything has an essence and it is the essence that is meaningful and eternal  These two aspects stalled the progression of the evolution thought  Essentialism became incorporated into Christian theology circa 500 CE (Common Era)  In the book of genesis, it was interpreted that it was the creations’ essences that were created  Through the middle ages there was little advancement of scientific knowledge  There were significant technological improvements in practical areas such as: agriculture, construction practices and warfare  Instead of scientific “investigations” there was a reliance on authority (this “authority” were sources such as the church and Aristotle)  Eventually there was an interaction between essentialism and Christian philosophy which gave rise “Natural Theology” of the renaissance  The important tenet of this set of concepts: “the world is a perfect creation of an intelligent, good, reasonable and divine Artisan – and that nature is like a book and that exists in parallel with the bible” o This implied that it was appropriate to study nature as if it were a literal book (can be viewed as conceited that humans thought that they would be capable of understanding the whole universe)  The thought was that the universe is operated by laws and is like a machine so it is humanity’s responsibility to know how to use it  By the end of the renaissance natural theology had developed to a point where there was a profound union between physical science and mainstream Christian theology  During this time and even into the Enlightenment world explorations continued venture out from Europe to other parts of the world o Marco Polo to china o The Portuguese to Africa and Asia o Columbus to where he “discovers” America on the behalf of the Spanish  These explorations revealed to Europe that there were numerous kinds of plants and animals in the world that were never mentioned in the bible or by Aristotle  This resulted in an erosion of authority  Now there was a new emphasis on an acquisition of knowledge and “facts” through observation and experimentation  This new emphasis would become encouraged through the Enlightenment  By the end of the 1700s there are still two questions about biology that the intelligentsia of Europe had still been unable to answer to complete satisfaction o 1: Is there a natural explanation and underlying “natural law” for why organisms are so well adapted to the environments in which they live? o 2: Why are there so many kinds (species) of organisms around the world that have nothing to do with humanity (either good or ill) and humanity can’t use them for anything?  There have been many throughout history that have tried to figure it out  The first comprehensive answer to these questions that gained any traction with the educated people was an evolutionary hypothesis that was put forward by a French biology professor: Jean-Batiste Lamarck  Jean-Baptiste Lamarck: (1 August 1744 – 18 December 1829) French naturalist who was also a soldier, biologists and academic o Lamarck was an early proponent of the idea that evolution occurred and proceeded in accordance with natural laws  Gave the term biology a broader meaning by coining the term for special sciences: chemistry, meteorology, geology and botany-zoology  When France was beginning to revamp the education system they pulled Lamark from hiding and hired him as a professor, just not in his own field of study  Lamarck’s ideas about evolution and change were published in 1801 o 1: Used animal physiology principles that were “cutting edge” for the end of the 1800s o 2: The popular notion of Scala Naturae (“The Great Chain of Being”) was supported  While this had already existed, Lamarck put an evolutionary spin to it  The Scala was based off of an observation made by Aristotle: animals could be arranged into a continuum  Simple plants  complex plants  plant-like animals  simple animals  complex animals  the perfect animal (humans)  By Enlightenment this continuum was interpreted as being a progression of created forms from simple to complex and finally becoming perfect  Lamarck’s interpretation of this idea was that the continuum represented an evolutionary process, not a creation process  The mechanism for origins of species would be spontaneous generation, life from non-life was not a new idea  Spontaneous generation: or anomalous generation is an obsolete body of thought on the ordinary formation of living organisms without descent from similar organisms. Typically, the idea was that certain forms such as fleas could arise from inanimate matter such as dust, or that maggots could arise from dead flesh. o 3: Inheritance of Acquired Characteristics  Based on an older idea from Hippocrates for the “use and disuse of parts”  Lamarck’s most famous example of Inheritance of Acquired Characteristic is demonstrated by “Larmarck’s Giraffes”  The ancestral giraffe had a shorter neck than the giraffes of today but it was accustomed to eating the leaves/twigs from trees  The giraffes that were able to stretch their necks to reach the foliage to eat would eat more than other giraffes that couldn’t stretch their necks or otherwise reach higher branches  Necks of stretching giraffes became longer and offspring inherited the longer necks  With this repeated over generations eventually all giraffes would have the longer necks  Lamarck’s hypothesis that adaptation occurs in natural populations by natural process was never accepted  The physiology aspect of the hypothesis was flawed  Scala Naturae was attacked by a professional and academic rival of Lamarck’s: Georges Cuvier o Cuvier showed that there was no continuum to what was called The Great Chain of Being o Each group of organisms (especially animals) were discontinuous in structure o Cuvier wasn’t so much in opposition of evolutionary thinking as he was a professional adversary of Lamarck  Had his own evolutionary theories  Georges Cuvier: 23 August 1769 – 13 May 1832 o French naturalist and zoologist o Sometimes called the “Father of paleontology” o Major figure in natural science research in the early 19th century o Instrumental in establishing the fields of paleontology and comparative anatomy through his work comparing fossils with living animals  Inheritance of Acquired Characteristics eventually became entirely rejected by natural historians and biologists  In the 1800s August Weissman showed conclusively that once the gonads of any animal develop, whatever happens to the rest of the body has no direct effect or influence upon the offspring  Inheritance of characteristic o will have become almost completely rejected by the end of the 1800s o resurface in early 20th century in Stalinist Russia in the form of “Lysenkoism” o 21st century “epigenetics” will be studied  Charles Darwin o 1809-1882, England o called the “Father of evolution” o was a naturalist who observed many species o wrote the book “The Origin of Species” o developed the theory of natural selection o Sailed to the Galapagos Islands on the ship, The Beagle, over the span of 1831-1836 o Heavily influenced by Charles Lyell and English geologist o Upon returning to England he indulged in a long period of writing up information on the specimens that he had collected o Didn’t immediately publish his views on evolution however  Darwin’s Theory of Evolution by Natural Selection  1. Variation exists among individuals in a species. 2. Individuals of species will compete for resources (food and space) 3. Some competition would lead to the death of some individuals while others would survive 4. Individuals that had advantageous variations are more likely to survive and reproduce.  Alfred Wallace o 8 January 1823- 7 November 1913 o English naturalist in southeastern Asia o Sent a manuscript to Lyell asking for him to sponsor Wallace for publication in England o Finally, a young English naturalist in southeastern Asia named Alfred Wallace sends Lyell a manuscript asking him to sponsor it for publication in England o Manuscript reveals conclusions identical to what Darwin has been telling Lyell for years privately o Influenced by Charles Darwin, Charles Lyell, Thomas Robert Malthus and Henry Walter Bates o Remembered as the “Father of Biogeography”  Wallace and Darwin jointly present a paper on evolution to the Linnaean Society of London in 1858  Presentation didn’t result in much of a reaction  Darwin went home and wrote a book entitled “On the origin of species by means of natural selection, or the preservation of favored races in the struggle for life.”  Darwin became famous/infamous while Wallace did not  Wallace continued to publish work concerning the distribution of animals and plants in Asia  There is a biogeographic feature called “Wallace’s Line” that delineates the Asian from the Australian biotas  Darwin launched a set of ideas that the reading public in Europe (and the U.S.) were ready for  Darwin’s starting point was “Artificial Selection”  Darwin’s eventual hypothesis from this starting point comes down to three observations and two conclusions: o Observations:  The populations of species and populations of all organisms show variation between individuals  Populations in nature tend to be stable (in numbers) from generation to generation  In every generation, more individuals are produced (by reproduction) than eventually survive. o Conclusions:  The environment selects those variants in every generation best fitted to survive and reproduce in that environment, and selects against those individuals less well-fitted to survive (the “principle of natural selection”)  Those variations favored by selection are somehow passed on to the next generation  This process will eventually produce adaptations by populations and species to specific environments  Darwin’s hypothesis will eventually become a theory in biology  Adaptation is produced by natural selection  Only natural selection can cause adaptation  The natural selection-adaptation process also causes the observed relationship between biological structures and their biological functions  This relationship isn’t always true though  Darwin also proposed that over time the adaptive process from natural selection will also result in the formation of new species of organisms o Populations of the same species living in different environments will gradually diverge from each other as they become adapted to the new environments o Divergence will result in a new species being formed out of the old species.  This explanation for the origin of species is apparently applicable to the speciation process in nature, but it is not a comprehensive explanation  There seem to be other evolutionary processes besides this one that can cause new species to come to existence  These will be proposed over the next 150 years  Principles of inheritance (today: “genetics”) weren’t understood by anyone at the time that Darwin’s book appears in 1859  Darwin’s best explanation for inheritance was something called pangenesis – that different parts of the body sent “messages” to the gonads, and these were somehow incorporated into the sperm and egg cells for transmission to the offspring  After Darwin’s idea were made public a great deal of research took place  By the late 1880s many other biologist “test” Darwin’s hypothesis using comparative means o Experimental methods weren’t used because the process of natural selection was presented as being a very gradual process  Prompted by the influence of Lyell’s uniformitarianist views on Darwin  Gregor Mendel: o 20 July 1822 - 6 January1884 o Moravian monk o Worked mostly in isolation on pea plants in an abbey located in what is now part of the Czech Republic o Published in obscure European journals which weren’t widely read in France or England o Works were not so much “unacknowledged” and their importance was not realized o Usually considered to be the founder of modern genetics  Around 1900 the importance of Mendel’s work was finally recognized by 3 botanists simultaneously o Dutch botanist: Hugo de Vries o German botanist: Carl Correns o Austrian botanist: Erich von Tchermark-Sysenneg  All were studying plant hybridization  Discovered Mendel’s principles, then they discovered Mendel’s publications  Corren and von Tchermark were interested agricultural applications of the work, but de Vries was interested in mutation.  Hugo de Vries o 16 February – 21 May 1935 o Somewhat reluctantly promoted Mendel’s discoveries o Enthusiastically promoted his own o Encouraged many others to take up what would be a new scientific discipline  Eventually called “genetics”  William Bateson o 8 August 1861 – 8 February 1926 o British plant scientist o Coined new biological terms  Genetics  Allelomorph (later shortened to allele)  Homozygote  Heterozygote  1901-1906: term “gene” began to emerge as the fundamental unit of inheritance  1902-1904: Sutton-Boveri Theory of Chromosomal Inheritance developed o Was developed by Theodor Boveri and Walter Sutton o Was able to associate the events of cell division (especially “reduction division”) studied by cytologists using microscopy with Mendel’s principles  Modern concept of a “gene”: “sequence of DNA that does something”  After 1910: explosion of genetic knowledge, major figure was Thomas Hunt Morgan  Thomas Hunt Morgan o 25 September – 4 December 1945 o American evolutionary biologist, geneticist, embryologist and science author o Won Nobel Prize in Physiology or Medicine in 1933 for discoveries elucidating the role that the chromosome plays in heredity o Morgan was the geneticist who was persuaded to work with a fruit fly, Drosophila melanogaster as an experimental animal for genetics.  Many discoveries in genetics that refined Mendel’s principles and discovered additional genetic principles and phenomena arose from the study of this insect  Downside of this emerging new field of genetics was the emphasis on mutation as a powerful evolutionary force  Over next 20 years genetics flourishes and evolution languishes  At about 1935 controversy between genetics and evolution comes down to three points: 1. Importance of mutation versus natural selection 2. Is all inheritance “hard” (immutable, fixed), meaning the genes of the organisms determine the phenotype and the phenotype is the organism’s fate 3. Gradual versus rapid (saltational) evolution  Result of the argument when some analysis by mathematicians (biometricians) involved with population genetics: the “Synthetic Theory of Evolution” (aka “New Synthesis”) o This set of ideas will merge Mendelian and Darwinian principles and concepts and almost reconcile them  The Synthetic Theory will reach the height of its popularity about the end of the 1950’s (it is sometimes called “NeoDarwinism).  The major concepts inherent in the Synthetic Theory were: 1. Biological variations arise by mutation (de Vries). 2. Hereditary transmission of genetic variation occurs by the principles of Mendel (Mendel and his heirs). 3. Adaptation by organisms to particular environments in which they live by a natural process (Lamarck) 4. Natural selection is the mechanism by which adaptation takes place (Darwin).  Some corollaries to the Synthetic Theory: A. Natural selection tends to act through tiny advantages and gradually changes populations. B. There is a long-term advantage for a population to possess variability – if the environment should change, then the variations previously selected against may now be selected for – and if they are not present, then extinction of the population (extirpation) may result. C. There is a selective advantage to having a harmonious arrangement of genes in chromosomes (or other genomic packaging, such as seen in prokaryotes). a. Fitness is measured in terms of differential reproduction, not differential survival (as per Darwin). D. Modern concept lies in how many of an individual organism’s alleles of its genes are contributed to the next generation by reproduction. a. Those individuals who have more offspring than others are thus more “fit” than those that have fewer offspring. E. Evolution is not a directed process, but instead is blindly deterministic –there is no goal, no purpose, no “teleology,” no progress in the evolution of organism.  Middle 20th century: o Synthetic Theory was embraced by biologists in general o Largely because it reinforced the link between biological structure and biological function o Virtually every biological feature at all levels of biological organization was under some type of natural selection o largely because it reinforced the linkage between biological structure and biological function, and that virtually every biological feature at all levels of biological organization was under some type of natural selection.  Enthusiasm for the Synthetic Theory would only last until about the 1960s when new questions arose: o How important are random events in the overall evolutionary process?  For example: “bottleneck events” have occurred where a large population of well- adapted individuals is abruptly reduced to a few individuals by a disaster that has nothing to do with that population’s general adaptiveness to the environment o Are most mutations at the molecular level selectively neutral?  Only variations that appear in the phenotype (that is, those mutations that are expressed) can be acted upon by natural selection.  Motoo Kimura (1968) proposed the “Neutrality Hypothesis” that strongly suggested that most mutations at the molecular level are indeed selectively neutral. “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.  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. Microevolutionary Processes  Definition of microevolutionary processes: evolution at the population level.  Gene versus allele: An allele is a form of a single specific type of gene. o Upper case letters for genes, lower case letters with subscripts to indicate individual alleles for that gene 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 experiment 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 genetics 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. 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.  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 Mutation 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 a1may mutate to a 2t one rate, but the back mutation rate from2a back to1a may well be different.  Mutation rates are not large numbers -6 o High mutation rate would be 10 mutations per genetic locus per generation. o Low rate would be 10 -1mutations 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  Concluding remark about mutation: Since mutations are often recessive, and appear in individuals in the heterozygous state, it may be a long time before the slow mutation rate will build up those mutant alleles in the population until they are numerous enough where heterozygous individuals will start, by chance, finding each other for mating. Natural Selection at the Population Level Four principles of, or conventions for, for natural selection  Principle 1: o Selection can affect attributes of organisms (elements of the phenotype) at any level of biological organization, from molecules and cells up to individuals o Selection operates on individual organism to increase or reduce their individual fitness  It is the population that evolves  What is population: For convenience, a population will be a “group of interbreeding individuals of the same species in a particular place and time.”  Principle 2: o Natural selection does not act on attributes of organisms that are not subject to inheritance  Example: acquired characteristics in the classical sense  Appreciation of variation in inherited attributes is essential to understanding how natural selection operates.  Some attributes will be the result of the action of a single gene, others by the actions of several genes acting together (polygenic).  A standard terminology for describing “attributes” utilizes the terms Character and Character States  Characters: gene-based (inheritable) features or attributes of organisms.  When discussing how characters appear in different species, it is important to restrict them to homologous characters – those inherited from a common ancestor.  The different forms of the attribute are the character states. o Example: if the character is “flower color” then the states could be red, pink, white, yellow, blue, green.  Discontinuous Character States (“discontinuously varying character states”) exits, such that there are no intermediate conditions between the states.  For the character “egg clutch size in pigeons”, the states can be 1 egg, 2 eggs, 3 eggs, etc.  Sometimes these states are governed by the expression of a single gene.  Continuously varying character states-associated with features with which there are many intermediate conditions between the states.  For example, the character of “ear length in kangaroo rats.”  The states could be 3.5mm, 3.51mm, or 3.51234 mm  These types of character states are often polygenic.  When plotted on a distribution of the appearance of the state against the number of individuals that possess each state, a bell-shaped curve is usually formed.  These data will have a mean value for the characteristic that can be shown on the curve.  Selection principle number 3:  Selection is thought to work in one of three ways on these types of character state distributions, these three ways are called the Modes of Selection. o Stabilizing Selection: (not the same thing as negative selection) is a type of natural selection in which genetic diversity decreases and the population mean stabilizes on a particular trait value. o Directional Selection: In population genetics, directional selection is a mode of natural selection in which an extreme phenotype is favored over other phenotypes, causing the allele frequency to shift over time in the direction of that phenotype. o Disruptive Selection: also called diversifying selection, describes changes in population genetics in which extreme values for a trait are favored over intermediate values. In this case, the variance of the trait increases and the population is divided into two distinct groups  Stabilizing Selection: o Many generations of selection against the individuals in the population at both extremes of the bell-shaped distribution of variation occurs. o The result, over time (many generations of the same stabilizing selection acting on this character in the same way) will produce a population in which more individuals are clustered around the mean value for the character and there are fewer individuals with extreme phenotypes for the character. o One would expect stabilizing selection operating in environments that are very stable over very long periods of time. o Selection acts against both “extremes” of the phenotypic distribution for the character  Example: very short ears and very long ears  Fitness of these individuals is accordingly reduced compared to the more common phenotypes that are closer to the mean value of the character  This type of selection should be associated with adaptation to very stable environments  Directional Selection o One of the extremes in the bell shaped curve of character state distribution is selected against – because of a change in the environment o Under directional selection, the advantageous allele increases as a consequence of differences in survival and reproduction among different phenotypes o The increases are independent of the dominance of the allele, and even if the allele is recessive, it will eventually become fixed  Was first descried by Charles Darwin in Origin of Species as a form of natural selection  A change in the environment causes one extreme of the phenotypic variation of a character in the population to be selected against o Example: against those with very short ears  Disruptive Selection o rarely observed.  The mean value of a character state, and those values clustered around the mean, are the states that are selected against over many generations.  An environmental change causes the phenotypes closest to the mean (and the majority of the population) to be selected against, while both phenotypic extremes are favored  Since most of the individuals in the population have character states clustered around the mean, the Disruptive Mode will most likely result in their being too few individuals with adequate fitness to sustain the population – it crashes into extirpation.  Rarely, a bimodal distribution of the character state will develop, with two means for each of the now abundant character states (if the character involves reproduction, two new species may form)  “Positive and Negative (Purifying) Selection”: Negative selection often invoked with Stabilizing Selection, Positive Selection with Directional Selection.  Natural Selection Principal Number 4: The simplest form of evolution is a change in allele frequencies of genes in a population over time.  The behavior of alleles in populations is the subject of the field of “population genetics,” and the principles of this field started with the Hardy-Weinberg Principle, aka The H-W Theorem.  Independently discovered in 1905 by Hardy & Weinberg.  The principle is this: If conditions for something called a “Hardy-Weinberg Equilibrium are met by a population of organisms, the allele frequencies of the genes in the population will not change from generation to generation (that is, there will be no evolution).  The conditions:  Panmixia (Random Mating): Random mating means that every individual in the population has an equal probability of mating with any other individual in the population (of the opposite sex). o In nature, on an individual mating basis, this seldom happens. o Sometimes, for example individuals will chose for mates those that resemble themselves phenotypically. o This departure from random mating is called Positive Assortative Mating, and will result in more homozygotes appearing in the next generation. o More rarely, there can be Negative Assortative Mating, where individuals choose mates that are phenotypically dissimilar to each other. o This departure from panmixia will result in more heterozygotes in the next generation. o In very large populations in nature, the relative mating success of individuals balances out, and panmixia is approached.  Large population size: How large? o Large enough not to cause changes in allele frequency to occur because of random forces (more later) o There is a related concept called “effective population size.”  No new copies of alleles are being added or subtracted from the population: These additions or subtractions can occur in three ways: o Mutation o Immigration of new individuals carrying new copies of alleles into the population o Emigration, individuals leaving the population and carrying their alleles with them.  Immigration and emigration are often cited here as causing “gene flow” (actually allele flow).  Predictions from the Hardy-Weinberg principle (in the above conditions are met):  Allele frequencies tend to remain constant from generation to generation.  Genotypes reach an equilibrium frequency in one generation and will remain at that frequency thereafter.  Allele frequency calculation:  To calculate allele frequencies for a gene, one must know: Population size (Number of individuals with each genotype.  Example of calculating allele frequency:  Population size = 500 individuals  Gene A with two alleles: a1 and a2  Three possible genotypic combinationsa1a2, a1a1, a2a2 are the three possible genotypic combinations o a1 1= 80 individuals o a1 2= 50 individuals o a2 2= 370 individuals  Total amount of alleles for gene A in the population: 1000 alleles  How many total alleles for a1: 80*2 + 50 = 210 alleles  How many total alleles for a2: 370*2 + 50 = 790 alleles  Allele frequency for a1 will be 210/1000 = 0.210  Allele frequency for a2 will be: 790/1000 = 0.790  By convention: o The frequency of the first allele (a1) is designated by p. o The frequency of the second allele (a2) is designated by q. o Such that p + q = 1.0 o And 1.0 - p = q o And 1.0 - q = p.  Going on the frequencies of the genotypes in the populations: o f(1 1 ) o f(1 2 ) o f(2 2 )  To make the prediction about the frequencies of the genotypes given the allele frequencies that are known for a gene, one must make an assumption that the separation of chromosomes at Meiosis I that will form the haploid gates is completely random with respect to which homologous chromosome goes into which daughter cell.  Therefore, each time a Meiosis I event takes place, it is independent of the other meiotic events taking place at the same time in the primary oocytes or primary spermatocytes.  Looking at a population, the probability that a sperm will have an a1 allele for gene A is going to be directly related to the frequency of the a1 allele in the population (the sexes will be equivalent in their production of gametes with a1 assortment of genotypes).  Therefore, the frequency of the allele can be used as an indicator of the probability of its being transmitted to the next generation.  The probability that any two given alleles will be united into a zygote are also equal.  Products of probabilities of independent events give you the combined probability of the events happening at the same time.  Since the frequency of the a1 allele in a population is p, then the probability of two a1 alleles coming together to form an a1a1 genotype will be the product of the frequencies: p x p = p2.  Therefore, the frequency of the a1a1 genotype in the next generation will be equal to its probability of occurrence (p2).  The probability for and the predicted frequency for the a2a2 genotype (in the next generation) will be q . 2 2  1.0 = p + q + f(a1a2)  Which can be resolved to:  1.0 = p + q + 2pq = (p + q)2  Where there are three alleles: (p + q + r)2 = 1.0  There will be six genotypes when there are three alleles.  The above expression expands to: p2 + 2pq + 2pr + q2 + r2 + 2qr = 1.0  Each of the terms of this expansion predicts a genotypic frequency in the next generation.  If there are four alleles, (p + q + r + s)2 = 1.0  How many possible genotypes? Use this formula: G = x(x+1)/2 where x is the number of alleles, and G is the number of genotypic combinations.  For four alleles, there are thus 10 genotypes. How allele frequencies change in a population due to natural selection GENOTYPE a1 1 a1 2 a2 2 N Before Selection 8000 1700 2300 N After Selection 7200 1300 2100 Survival Rate = γ 7200/8000 1300/1700 2100/2300 γ = 0.900 γ = 0.764 γ = 0.913 1,1 1,2 2,2 Relative Fitness, W 0.900/0.913 0.764/0.913 0.913/0.913 (compared to most W 1,1 0.986 W 1,2=0.837 W 2,2 1.00 successful genotype, that of 2 2 ) Selection Coefficient, s 0.014 0.163 0.0 (s = 1- W)  Allele frequencies of the population before and after selection  Don’t need before selection [N = 12,000, p = 0.738, q = 0.262] what we need to work with is the allele frequencies after selection, where  N = 10,600  p = 0.741  q = 1-p = 0.259  Where we want to go with this – starting with these allele frequencies with the selection regime values for W and s that we just calculated for each genotype continuing into the next generation – what will be the allele frequencies in the next generation after this one?  First, we need to consider the last item on the worksheet - “Mean Fitness of the Population” (W-bar)  Calculated by this expression: p2W1,1 + 2pqW1,2 + q2W2,2  The sum of each the predicted genotypic frequencies multiplied by the relative fitness of each of those genotypes. For the example in the above data table: 2 2 o (0.741) (0.986) + 2(0.741)(0.259)(0.837) + (0.259) (1.0) = Mean Fitness of Population = 0.5414 + 0.3213 + 0.0671 = 0.9298  Once we have calculated the Mean Fitness of the Population, we can then go to predicting allele frequencies in the next generation should those genotypic fitness values remain the same  The selection intensity on each genotype stays the same). Four cases of dominance: 1. Complete dominance: where a is1completely dominant and (unlike the above data sheet), 1 1 genotype will be the optimal genotype.  W = 1.0 W = 1 – s W = 1.0 1,1 2,2 1,2 2. Complete recessivity – where a 1s completely dominant, but there is selection againsts the dominant allele. The optimal genotype will be the recessi2 2a a .  W 1,1-s W 1,2= 1-s W 2,2 1.0 3. Semi-dominance (Incomplete Dominacne) - where the a all1le is semi-dominant, so that there is “dosage effect” to the selection agains2 the a allele. The optimal genotype will be a1 1.  W 1,1.0  W 2,2-s  W 1,2 1 –s/2 4. Overdominance (aka heterosis). There is selection against homozygotes, and the optimal genotype is the1 2a heterozgyote.  W 1,2.0  W 1,1 1-s  W 2,2 1-h  “h” is a second selection coefficient, as the two homozygote genotypes are probably under different selection intensities).  This final equation for the change in allele frequency under conditions of complete dominance of the first allele is much simpler than the original equation for such change.  In this second case, also, the dominance condition greatly simplifies the original equation in allele frequency change from one generation to the next when alleles are under selection.  In the semi-domiance case, there is the greatest simplification of the original equation. Essentiallly, possessing as single copy of the recessive allele being selected against at some level is only “half as bad” for the heterozygous genotype as having two copies of the inferior allele.  Overdominance (heterosis): final dominance case and newest one to be introduced  In this case, the classic case of overdominance in human genetics is produced by a recessive allele that causes sickleheterozygote is the optimal genotype, and both homozygotes are disfavored by selection.  Cell anemia: Sickle-cell anemia is caused by the homozygous recessive genotype for this allele. In environments where human malaria infections are prevalent, heterozygosity for the sickle-cell allele carries with it some resistance to malaria infections.  Under these conditions, the heterozygote is the “optimal genotype.”  The fitness disadvantage of being homozygous dominant is slight compared to the harsh selection against the homozygous recessive condition.  Thus there must be two distinct (different) selection coefficients (s and h) for each homozygous genotype.  What is important here is the predictions that are derived from these equations.  A dominant allele favored by selection quickly replaces a recessive allele not so favored.  But a recessive allele favored by selection takes a long time to build up in the population before homozygous individujals reach a level of abundance where replacement of the unfavored allele becomes rapid.  Semidominance: where the dominant allele is selected for, the heterozygote condition is selected for half as much as the dominant homozygote, has the fastest replacement rate to fixation.  When graphed, the change in allele frequencies for the three cases looks like this: Natural selection at the population level  Failure of reproduction is a kind of “genetic death” where the potential population size is not realized.  Genetic death can be thought of as “burden” on the population – that reproductive potential not realized because of this “burden” is called genetic load.  Mathematically: W max= Relative fitness of the optimal genotype. Four types of genetic load under different selection regimes  Mutational Load: This load arises from selection against deleterious mutations.  In every generation o a) dominant mutations are removed as they appear if they are deleterious o b) recessive mutations appearing in the homozygous state are selected against. Stabilizing selection is operating here.  Segregational Load: Balancing selection acts to promote heterozygotes at the expense of less-fit homozygotes – characteristic of overdominance (heterosis).  Example: sickle-cell anemia.  Misplaced Individual Load: In a heterogeneous environment, some individuals will make their way into subniches for which they possess inappropriate phenotypes.  These individuals do not reach their full reproductive potential. If this happens, Stabilizing Selection may be promoted, but, more likely, Disruptive Selection may result.  Substitution Load: occurs under Directional Selection. Losses at one end of the character state (phenotypic) bellshaped curve are replaced by additions the other end of the curve.  In terms of the two-allele model, replacement of one allele carries “genetic death” for the individuals possessing it, but a “substitution” with the favored allele occurs.  The process can be very expensive for the population in terms of genetic load if the old allele was very abundant when the directional selection process began.  Expensive, that is, in terms of “genetic death.”  Also, if selection for alleles or combinations of genes occurs directionally, the process will be even more expensive.  However, genetic load implicates alleles under selection only. Data from isozymes (electrophoretic phenotypes representing putative alleles) from natural populations of eukaryotes reveal that some populations of species are extremely polymorphic at the allelic level (that is, they show high levels of heterozygosity) for several structural gene (enzyme-producing) loci.  These alleles are probably selectively neutral (in the sense of Kimura’s hypothesis), as there seems to be no segregational load involved.  These predictions and observations bring us to the “Cost of Selection,” which ties selection and load together – a concept originally proposed by J.B.S. Haldane, one of the architects of the “Synthetic Theory.”  Haldane’s concept about genetic deaths that were required to completely replace one allele disfavored by selection by a second allele favored selection (i.e., Directional Selection) has the following two components:  1. The number of genetic deaths required to replace an allele is always greater than the population size in any single generation.  2. The actual relationship between the population size and the number of genetic deaths involved is represented by a cost factor. The cost factor depends heavily upon the initial frequency of the favored allele, and the rate of replacement of the other allele. The rate of replacement is affected by s (selection coefficient), which is derived from the Relative Fitness of genotypes (e.g., W1,1), and the Mean Fitness of the Population. o Haldane found that the number of genetic deaths to complete the substitution of an old allele will be 10 to 20 times the number of breeding individuals in the population (usually), but it can go as high as 100 times the number of breeding individuals. o Selection pressure may be too great (Cost of Selection too high) and exterminate the


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