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Bio 102 Week 2 Notes

by: Denice Arnold

Bio 102 Week 2 Notes BIOL 102

Denice Arnold

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Chapters 22, 23, and 24 of Life: The Science of Biology.
Biological Principles II
Dr. Sniegowski
Class Notes
Biology, Bio, Bio102
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This 8 page Class Notes was uploaded by Denice Arnold on Thursday January 28, 2016. The Class Notes belongs to BIOL 102 at University of Pennsylvania taught by Dr. Sniegowski in Spring 2016. Since its upload, it has received 18 views. For similar materials see Biological Principles II in Biology at University of Pennsylvania.


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Date Created: 01/28/16
Bio Chapter 22 Saturday, January 23, 2016 10:04 PM Chapter 22 Life: The Science of Biology (p. 449 - 464) Reconstructingand Using Phylogenies Phylogeny - history of evolutionary relationships among organisms or their genes Phylogenictree - diagram that portrays a reconstruction of that history Common ancestor of all organisms in the tree form the root Order of nodes along the horizontal axis indicates timing order Vertical distances do not mean anything Taxon - group of species A taxon that consists of an ancestor and all of its evolutionary descendants is called a clade Sister species are species that are each other's closest relatives Sister clades are clades that are each other's closest relatives Two or more species that have been inherited from a common ancestor are said to be homologous Ex: the vertebral column is homologous in all vertebrates An ancestral trait is present since the ancestor A derivedtrait differs from its ancestral form Synapomorphiesare shared, derived traits Similarity in traits does not necessarily indicate relatedness Convergentevolution - occurs when independently evolved traits are subjected to similar selection pressures Ex: wing bones of bats and birds Evolutionaryreversal - occurs when a trait reverts from a derived state back to an ancestral state Ex: ancestor frogs had teeth that most modern frogs lack; a species in South America has regained these teeth Homoplasies- traits that are generated by convergent evolution or evolutionary reversal PhylogenicTrees If a trait is present in both the ingroup, the group of interest, and the outgroup, a species closely related to the ingroup, then the trait must be ancestral Derived traits are only present in some members of the ingroup Parsimony states that the preferred explanation of our observations is the simplestexplanation Best hypothesis requires the fewest homoplasies Morphology - the presence, size, shape, and other attributes of body parts Important for phylogenetic analysis An accurate analysis often requires further information Many species look similar, but differ in behavior and physiology In addition, some morphological variation is due to environment, not genetics Development - developmental pattern similarities indicate evolutionary relationships Ex: larvae of sea squirts and vertebrate animals have a flexible gelatinous rod in the back Can infer that sea squirts are more closely related to vertebrates than initially expected Paleontology - fossil record Can distinguishancestral from derived traits Can reveal where lineages diverged Behavior - genetically determined behavioral traits are useful in phylogenetic analysis Molecular data - heritable variation is encoded in DNA Complete genome, that contains traits, is useful in phylogenetic analysis Genes can be found in the nucleus (DNA),mitochondria (mtDNA), as well as chloroplasts (cpDNA) Molecularclocks - average rate at which a given gene or protein accumulates changes Used to gauge when a particular split in phylogeny occurs Calibrated using independent data - fossilrecord, known times of divergence, biogeographic dates RelatingPhylogenyto Classification Genus - a group of closely related species Families are grouped into orders, orders into classes, classes into phyla, and phyla into kingdoms A taxa contains an ancestor and all descendants and no other organisms Monophyletic- every taxon should be a complete branch on the tree of life Monophyletic groups can be removed from the tree with a single "cut" Polyphyletic- group that does not include its common ancestor Paraphyletic - group does not include all descendants of a common ancestor Both poly and paraphyletic groups are not considered appropriate taxonomic units Bio Chapter 23 Sunday, January 24, 2016 4:03 PM Chapter 23 Speciation (Life: The Science of Biology p. 467 - 482) Speciation Speciation- the divergence of biological lineages that results in reproductive isolation Morphological species concept - classification based on appearance alone Assumption that a species compromises individualsthat look alike Two main limitations Members of the same species don't always look alike Ex: males vs females, young vs old Two species that are indistinguishablemay not interbreed Biological species concept - species are capable of interbreeding and are reproductively isolated from other populations Reproductiveisolation - most important factor in divergence of lineages Genes are no longer exchanged Lineage species concept - considers species over evolutionary time Ancestor-descendant series of populations are followed over time Ends with extinction or another speciation event Lineage splitting is gradual (thousands of generations) Ancestral lineage may be splitwithin a few generations (ie. polyploidy) These three concepts can be used in conjunction Genetic Basis of Speciation Speciation requires an interruption in gene flow within a species Early geneticists sought to explain how a reproductively incompatible allele could arise without being able to be introduced into the species through reproduction Dobzhansky-MullerModel Assumed that a singleancestral population is subdivided into two separate populations by some barrier to gene flow ie. formation of a new mountain range, a flood These two populations would evolve independently A new allele would arise and become fixed The key is that there needs to be at least two loci After genetic changes, they may still be able to interbreed, but the offspring would have inferior, or even lethal, genes Chromosomal arrangements that arise can also lead to genetic incompatibility Genetic incompatibility develops over time Barriersto Gene Flow Allopatricspeciation - populations divided by a physical barrier Dominant mode of speciation Could be a body of water, a mountain range, etc. Form when continents drift, sea levels rise and fall, glaciers advance and retreat, climates change, etc. Usually form two sisters species on each sideof the geographic barrier Also occurs when new members of a population cross an already existing barrier Sympatric speciation - occurs without physical isolation, usually a gradual process Disruptive selection - individuals with different genotypes have a preference for distinct microhabitats where mating takes place Ex: apple maggot flies used to mate on hawthorn fruits, but 150 years ago, when apple trees were introduced, the population diverged into two different species, one who mates on hawthorn fruits, and one who mates on apples Polyploidy - duplication of sets of chromosomes Most common means of sympatric speciation (especially among plants) Autoploidy - polyploidy in a singlespecies Ex: two accidentally unreduced diploid gametes combine to form a tetraploid individual Tetraploid and diploid individuals of the same species are reproductively isolated because their offspring are usually sterile triploid individuals (whose chromosomes do not segregate evenly during meiosis) Allopolyploidy - combining chromosomes of two different species Ex: individualsof two different (but closely related) species interbreed Disruption of normal meiosis, resulting in chromosomal doubling Often fertile, each chromosome has a nearly identical pair When Newly Formed Species Come into Contact Reproductive isolation may be incomplete when newly formed species come back into contact If hybrid individualsare less fit than non-hybrids, then selection will favor parents that do not produce hybrid offspring Reinforcement- strengthening of mechanisms that prevent hybridization Prezygotic isolating mechanisms - mechanisms that prevent hybridization Postzygotic isolation mechanisms - mechanisms that reduce the fitness of hybrid offspring Prezygoticisolatingmechanisms Mechanical isolation - differences in the sizes and shapes of reproductive organs that may prevent that union of gametes from different species Ex: in plants, mechanical isolation may involvea pollinator Temporal isolation - distinct mating seasons do not coincide, resulting in no opportunity to hybridize Ex: three closely related leopard frog species breed at different times of the year Behavioral isolation - individualsmay reject or fail to recognize potential mating partners Ex: female frogs respond to the mating calls of their own species and ignore even the calls of closely related species Habitat Isolation - two closely related species evolve preferences for living or mating in different habitats May never come into contact during their respective mating periods Ex: Rhagoletis flies or the cichlid fish Gametic Isolation - sperm of one species may not attach to the eggs of another or may be chemically incompatible Especially important for aquatic species that release their gametes directly into the environment environment Postzygotic isolatingmechanisms Low hybrid zygote viability - hybrid zygotes may fail to mature normally Not reproductively capable adults Low hybrid adult viability - hybrid offspring may have lower survivorship than non-hybrid offspring Hybrid infertility - hybrids may mature into infertile adults Generally, sympatric populations form a more effective prezygotic reproductive barrier, leading to more divergence, than allopatric populations Natural selection appears against hybridization in areas of sympatry Hybrid zones may form if reproductive isolation is incomplete Closely related species may hybridize in areas where their ranges overlap These zones contain recombinant individualsresulting from many generations of hybridization Hybrid zones do not get wider over times due to a strong selection against hybrids (suffer from a range of defects, many of which are lethal) Rates of Speciation Many factors influence speciation, giving rise to a variation of rates of speciation Diet specialization - populations with more specialized diets may be more likely to diverge, giving rise to faster rates of speciation Pollination - speciation rates are faster in animal-pollinated than in wind-pollinated plants Sexual selection - mechanisms of sexual selection results in high rates of selection Sexual dimorphism- males look distinctly different from females Sexually dimorphic clades have higher rates of speciation than do monomorphic clades This is because animals with complex sexually selective behavior make sophisticated discriminations among potential mating partners Dispersal ability - poor dispersal abilities usually results in higher speciation rates Evolutionaryradiation - the rapid proliferation of a large number of descendant species from a single ancestor species Occurs when a species colonizes a new area that contains no other closely related species Adaptive radiation - when evolutionary radiation results in an array of species that live in a variety of environments and differ in the ways they exploit those environments Ex: on the Hawaiian islands,land snails,insects, birds have all undergone adaptive radiation Bio Chapter 24 Sunday, January 31, 2016 4:30 PM Chapter 24 Evolution of Genes and Genomes (Life: The Science of Biology p. 485 - 502) Genomes and Evolution Genome - full set of genes plus noncoding regions of DNA Molecularevolution - this field investigates the mechanisms and consequences of macromolecules (particularly DNA and RNA) and proteins The Central Dogma of molecular biology DNA --> mRNA (transcription) --> protein (translation) Coding sequences follow the genetic code Amino acids that make up proteins are specified by triplets of base pairs The amino acid code is redundant (multiple sequences per amino acid) Highlyrepetitivesequences are short, noncoding sequences that are repeated hundreds of times in tandem The vast majority of the genome is not coded Moderatelyrepetitivesequences include RNA genes and transposons Transposons have the ability of replacing themselves in the genome Gene number varies widely But a larger genome does not always indicate greater complexity Ex: rice has 3x the number of genes than we do The total genome size varies even more widely Differences in genome size are not so variable of we only consider the portion of DNA that is actually encoding Most variation lies in the amount of noncoding DNA What matters is the number of ways genes are put together Alternative splicing- how many ways can the exons be alternatively expressed Expression control of those genes alsoprovides variability The Human Genome We are able to recover signatures of evolution in DNA Strongly conserved sequences can indicate evolutionary constraint 5% of the human genome is conserved across mammals 1.5% of our genome codes for proteins 3.5% encode regulatory elements The other 95%? Junk Selfish DNA that does not harm, but adds more meaningless code Reproduces faster than the host genome Theory by ENCODE (ENCyclopedia of DNA Elements) 80% of human genome contains sequence elements linked to biochemical function Created controversy in this field Evolutionof Gene Number Evolutionof Gene Number Mechanisms that change gene number Transference from other species Lateral gene transfer - allow individual genes, organelles, or fragments of genomes to move horizontally from one lineage to another Some species may pick up fragments of DNA directly from the environment Other genes may be picked up in a viral genome and transferred to a new host when the virus becomes integrated into the host's genome Hybridization between species also results in lateral gene transfer Depictions of lateral gene transfer events on the underlying species tree are known as reticulations Most lateral gene transfer occurs among bacteria Duplication within species results in four fates 1. Both copies of the gene may retain original function 2. Both copies retain original function, but the expression of the genes may diverge 3. One copy of the gene may be incapacitated by the accumulation of deleterious substitutions and become nonfunctional or eliminated 4. One copy of the gene may retain its original function while the second performs a different function Several successive rounds of duplication and mutation may result in a gene family - a group of homologous genes with related functions Entire genomes are duplicated in polyploid organisms Massive opportunities for new functions to evolve Ex: evolution of jawed vertebrates Jawed vertebrates have four Orphan genes - stretches of sequence expressed that don't actually code for proteins Genes that are found only in one species are orphan genes InferringSelectionThrough Gene SequenceEvolution Mistakes in DNA replication/repair provide the raw material for evolutionary change When point mutations (A --> G) go on to fixation, they become substitutions Synonymousor silentsubstitutionsdo not change the specified amino acid Nonsynonymoussubstitutions do change the specified amino acid Relative rates of synonymous and nonsynonymoussubstitutions vary Neutral amino acid replacements - two rates are similar Positive selection for change - rate of the nonsynonymoussubstitutions are expected to be higher than synonymous Purifying selection - rate of synonymous substitutions should be higher than nonsynonymous


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