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203 Cards in this Set
- Front
- Back
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Homology
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any similarity between characteristics that is due to their shared ancestry (forelimbs)
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Evolution can be viewed as
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a series of bifurcations in a phylogenetic tree- all life can be traced back to a common ancestor
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attributes derived from
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a common ancestor
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once related lineages are reproductively isolated, evolution can lead to
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modifications of the basic plan
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future evolutionary paths are constrained by
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past history
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Systematics
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establishes the genealogical relationships among organisms by reconstructing phylogenies
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Systematics seeks to (3 goals)
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1) catalog and name the diversity of life
2) discover the phylogenetic relationships among species 3) to classify species into more inclusive groups |
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Linnaeus contributions
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binomial nomenclature, hierarchical system of classification
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levels of hierarchical system of classification
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Kingdom, Phylum, Class, Order, Family, Genus, Species
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taxonomy
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the naming and classification of organisms
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Why has systematics become a rigorous scientific discipline over the past two decades?
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the advent of molecular genetic methods and the development of an explicit conceptual framework for reconstructing phylogenetic trees
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Phylogeny
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a Hypothesis which reflects evolutionary relationships. These relationships are best viewed as a branching pattern depicting a sequence of ancestor-dependent relationships
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Terminal
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a taxonomic group (like a species or gene); end of branch
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Branches
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the lines in a phylogenetic tree that connect terminal nodes or one node to another
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Nodes
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where branches intersect; they represent ancestors of all terminal taxa that descend from them.
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MRCA
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most recent common ancestor; the last ancestor shared by a group of terminals; nodes in the tree are MRCAs of all terminals connected to them
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Clades
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natural groups of organisms, genes, or proteins in a phylogenetic tree; in example tree: any MRCA and all of the terminals that descend from it
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Root
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the MRCA of the ingroup (point of attachment that connects the ingroup and the outgroup)
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Character
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a feature common (homologous) to all terminals sampled (e.g. eye color; base #432 in a gene)
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Character state
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what a character looks like in an individual (e.g., eyes are blue; base #432 is an A)
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important in constructing trees
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Relative branching order, NOT the orientation
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Monophyletic groups (clades)
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contain all the descendants of a single common ancestor
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polyphyletic groups
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do not contain the most recent common ancestor of its members
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paraphyletic groups
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exclude descendent taxa
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only ___ groupings should be used to classify organisms
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Monophyletic
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The number of possible trees increases...
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exponentially as the number of taxa increases
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Phylogenetic Inference: We need homologous traits that are shared among species and...
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are similar because they were modified in a common ancestor. We call such a trait Synapomorphy
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Synapomorphies
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Shared, derived characters
Define Branching points Homologous characters that reflect descent from a common ancestor |
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Synapomorphies: when genetic separation occurs, species form, and
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homologous traits undergo changes due to evolutionary mechanisms such as mutation, selection, or genetic drift.
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Synapomorphies are nested...
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as you move through time and trace a tree from the root, each branching event adds another derived trait
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cladogram
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phylogeny based on synapomorphies
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Autamorphies
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Characters that are unique to a single taxon are uninformative for assessing the phylogenetic relationships among groups
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Pleisiomorphies
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Shared primitive characters are useless for reconstructing the phylogenetic relationships among taxa (everyone has it= no discriminatory power)
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Homoplasy
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-when shared traits are not due to inheritance from a common ancestor
-flippers in penguins and seals (convergent evolution) -Reversals -Prevent accurate reconstruction of phylogeny |
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Homoplasy: Derived tratis can also mutate back to a primitive form
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=reversals
-ex. A can mutate into a T during a mistake in replication and unite two taxa, but it can also mutate back to an A |
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what causes Homoplasy
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Convergent evolution
Parallel Evolution Evolutionary Reversals |
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Convergent Evolution
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distinct phenotypes *converged* on the same phenotype, but that the ancestral phenotype giving rise to the convergence was not shared (bat and bird wings)
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Parallel Evolution
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Implies that the same phenotype evolved in two separate lines from the same ancestral phenotype. (not sure occurs at morphological level, but likely at DNA level)
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Evolutionary Reversals
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the return of a derived character state to an ancestral character state
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Parsimony
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A criterion for selecting alternative hypotheses based on minimizing the total among of change or complexity
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methods to estimate phylogenies
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Parsimony and others
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what to do with phylogeneies
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-classification
-Distinguish homology from analogy... evolution of traits (e.g. character evolution studies) -Molecular clocks and rates of evolution -Biogeography -Phylogeography (population history of a species) -Coevolution (do species cospeciate) -Disease evolution and transmission |
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Biogeography
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-Seeks to understand why certain species are only in certain parts of the world
-Have distributions of animals changed through time? |
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ultimate source of new genetic variation
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mutation (raw material for evolution)
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Mutation is the only process that creates
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new alleles
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Environmental factors (UV, chemicals, radiation, viruses) may
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influence mutation rate, but not likely the direction of mutation (i.e., mutations are random with respect to their ultimate function)
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Mutation may be ____ with respect to position in genome
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nonrandom
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only ____ mutations are passed on, not ____ mutations
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germline; somatic
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Point mutations (substitutions)
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alters single point in the base sequence
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point mutations caused by
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error during replication or DNA repair
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Point mutations: Transitions more common than transversions because
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less disruption of DNA helix
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Effects of point mutation: Synonymous (silent) mutations
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code for the same amino acid
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Effects of point mutation: Nonsynonymous (replacemnt) mutations
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code for a different amino acid (sickle cell GAG to GTG)
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Effects of point mutation: nonsense mutations
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code for a stop codon and can truncate the protein (likely results in loss-of-function)
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Point mutations can...
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mutate back to original state
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Insertions and deletions (indels)
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mutations in which an extra base pair(s) are inserted into a new place in the DNA or a section (one or more base pairs) of DNA is lost, or deleted
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Insertions and deletions; caused by
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error during replication, especially over repeated DNA. Also, when transposable elements move within the genome, or by viruses.
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effect of insertions/deletions
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cause a frameshift in coding sequence (change in reading frame)
-difficult to revert back to original state |
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Transitions
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from A-T or C-T (point mutations)
more common |
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Transversions
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Purine-Pyrimidine (point mutations) less common
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Gene duplications
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create copies of whole genes
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Gene duplications caused by
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1. Tetrotransposition (mRNA reverse transcribed and incorporated back into DNA)
2. Unequal cross over (error in homologous recombination) |
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what happens to duplicated genes?
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the second copy of the gene is often free from selective pressure (i.e., mutations have no deleterious effects to its host organism because still have original gene that is functional)
-Thus, likely to diverge from parent sequence -May become non-functional (e.g., gets nonsense mutation) -May take on new function |
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Deleterious
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reduce fitness of individual
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Paralog
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homologous genes that diverge within the same genome (within a species as result of gene duplication event)
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Ortholog
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homologous genes that diverged after speciation (between species)
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Meiosis Review
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1. Points of crossover are potential source of error to create mutation
2. Also alignment of homologs 3. recombination reshuffles gene combinations (does not create new genes) |
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Inversions
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mutation that affects gross morphology; results when a chromosome segment breaks in two places, flips, and reanneals
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Inversions have important impacts
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-Gene order becomes reversed
-This affects genetic linkage -May prevent recombination --so genes stay in combination -Or get crossing over, but results in large duplications or insertions |
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Inversions can play a significant role in evolution
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-if no recombination then the alleles of different genes locked together. Inherited as "supergene"- selection on groups of genes
-ex. fruit flies (small body size better in hot dry areas, associated with chromosome inversion) |
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Genome Duplication
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entire genomes can be duplicated
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polyploid
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organisms have >2 chromosome sets (humans=diploid)
(tetraploid, hexaploid, octoploid, etc.) |
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genome duplication common in
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plants (possibly due to self-fertilization)
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genome duplication can
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create new species that is reproductively isolated from parent species in single generation
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genome duplication creates
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genome wide duplications of genes- lot of new genetic material to evolve and possible gain new function
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once thought that ____ were similar among organisms
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mutation rates
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mutation rate based on
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observable phenotypes
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gene duplication and genome duplication rates are relatively
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high
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with _____ mutation rate research is expanding
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new sequencing technologies
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many mutations are likely
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harmful or neutral (silent mutations or noncoding DNA)
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Many mutations affect _____ while much evolutionary change involves____
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a single protein product (or a small set of related proteins produced by alternative splicing of a single gene transcript) while much evolutionary change involves myriad structural and functional changes in the phenotype
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How can the small changes in genes caused by mutations lead to the large changes that distinguish one species from another?
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can have mutations in genes that control developmental pathways. One gene has control over many downstream processes.
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Regulatory mutations (in Sticklebacks) in major developmental control genes
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may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.
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Mendel's Laws
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Law of Segregation (the First Law)
Law of Independent Assortment (The Second Law) |
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The Law of Segregation
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states that when any individual produces gametes, the copies of a gene separate so that each gamete receives only one copy. A gamete will receive one allele or the other. This is meiosis. In Meiosis the paternal and maternal chromosomes get separated and the alleles with the characters are segregated into two different gametes
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The Law of Independent Assortment
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states that alleles of different genes assort independently of one another during gamete formation. This is due to Recombination or because Genes are on Separate Chromosomes.
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Homozygous
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having 2 of the same alleles, AA or aa
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Heterozygote
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have 2 alleles that are different, Aa.
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observed heterozygosity
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frequency of Aa
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evolution
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change in allele frequencies over time
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population genetics tracks
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the fate, across generations, of genes in populations
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population genetics is concerned with
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whether a particular allele or genotype will become more or less common over time, and WHY
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population
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a freely interbreeding group of individuals
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gene pool
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the sum total of genetic information present in a population at any given point in time
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phenotype
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a morphological, physiological, biochemical, or behavioral characteristic of an individual organism
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genotype
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the genetic constitution of an individual organism
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locus
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a site on a chromosome, or the gene that occupies the site
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gene
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a nucleic acid sequence that encodes a product with a distinct function in the organism
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allele
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A particular form of a gene
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allele (gene) frequency
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the relative proportion of a particular allele at a single locus in a population (between 0 and 1)
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genotype frequency
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the relative proportion of a particular genotype in a population (between 0 and 1)
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for two mutually exclusive events, the probability of EITHER occurring is
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the sum of their individual probabilities
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the probability of two independent events occurring is
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the product of their individual probabilities
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the sum of genotype frequencies
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=1
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sum of allele frequencies
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=1
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two populations with markedly different genotype frequencies can have
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the same allele frequencies
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the allele frequencies will be
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what is in the gamete pool (gene pool)
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allele frequencies will stay the same
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so will the genotype frequencies after one generation of random mating
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Hardy-Weinberg equation
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(p^2) + 2pq + (q^2) = 1
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Hardy Weinberg Law (1908)
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1. The frequency of alleles does not change from generation to generation; in other words, the population does not evolve
2. After one generation of random mating, offspring genotype frequencies can be predicted from the parent allele frequencies. A single generation of random mating establishes H-W. -A single generation of random mating establishes H-W equilibrium genotypic frequencies and neither these frequencies nor the gene frequencies will change in subsequent generations of random mating |
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H-W assumptions
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1. All individuals have equal probabilities of survival and reproduction
2. The population is infinitely large (no genetic drift) 3. Genes are not added from outside the population (no gene flow or migration) 4. Genes do not change from one allelic state to another (no mutation) 5. mating is random |
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assumptions 1-4
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will change allele frequencies
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Assumption 5
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only changes genotype frequencies
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The H-W can be extended to
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Loci with >2 alleles
-as long as organisms are diploid |
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Implications of the H-W principle
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1) A random mating population with no external forces acting on it will reach the genotype equilibrium H-W frequencies in a single generation, and these frequencies remain constant thereafter
2) any perturbation of the allele frequencies leads to a new equilibrium after random mating 3) the amount of heterozygosity is maximized when the gene frequencies are intermediate |
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2 pq has a maximum value of 0.5 when
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p=q=0.5
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a rare allele is more common
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in its heterozygote form
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4 primary uses of the H-W principle
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1) enables us to compute genotype frequencies from generation to generation, even with selection
2) serves as a null model in tests for natural selection, nonrandom mating, etc. by comparing observed to expected genotype frequencies 3) forensic and disease risk analysis 4) expected heterozygosity provides a useful means of summarizing the molecular genetic diversity in natural populations |
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If the null hypothesis is true (i.e., we are in H-W equilibrium)
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we would expect a sample of this size to show this much (or more) of a departure from expectations (purely by chance sampling) less than 5% of the time
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if we reject the null hypothesis
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one or more of the assumptions of the H-W principle are not satisfied in this population
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polymorphism
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the proportion of loci polymorphic (ie > 1 allele)
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Heterozygosity
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proportion of heterozygotes in a population at a single locus or proportion of loci heterozygous in an individual genome
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Monomorphic Locus
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all individuals fixed for same allele
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Polymorphic locus
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2 or more alleles
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expected heterozygosity
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the probability that any two alleles chosen randomly from the total population are different (slide 9 from lecture 10)
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Natural selection violates...
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the H-W assumption that all individuals survive at equal rates and contribute equal numbers of gametes to the gene pool
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Absolute fitness (W) of a genotype
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the produce of the proportion survival to maturity times the average fecundity (remember lxmx)
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W can be calculated as
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the ratio between the number of individuals with that genotype after selection to those before selection (this is only viability selection)
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whether a particular absolute fitness is high or low depends on
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the values of other genotypes in the population. We need a second measure of fitness that accounts for this
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Relative fitness (w) of a genotype
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the fitness of a genotype compared with others in the population
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w can be calculated by
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dividing the genotype's fitness by the highest fitness in the population
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Dominance
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phenotypic effect of one allele completely "masks" the other in heterozygous combination
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Selection coefficient (s)
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fitness disadvantage to (or strength of selection against) a genotype s=1-w
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Less fit recessive alleles
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can continue to exist for some time in populations in heterozygotes, even when they are lethal in the homozygous condition. After many generations, these less fit alleles would be expected to disappear
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Because of its low frequency, a more fit recessive allele will
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be present only in heterozygotes initially and it may disappear from the population altogether. However, if it gets to a high enough level in the population to result in homozygous recessives, the frequency of the more fit recessive allele will quickly increase because it is now exposed
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Less fit dominant alleles vs. less fit recessive alleles
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less fit dominant alleles are removed more quickly and completely while less fit recessive alleles may remain in the population at low levels because they can "hide" in the heterozygote
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natural selection removes less fit alleles from populations but the
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manner depends on if they are dominant or recessive
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populations under selection evolve towards
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higher population mean fitness
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Heterozygote advantage
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also known as overdominance, or Heterosis, results in a stable, polymorphic equilibrium
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Varying selection
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If selection varies spatially or temporally, polymorphism may be maintained
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Frequency-dependent selection
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the fitness of the genotype depends on its frequency in the population. If common genotypes have low fitness, then the polymorphism will be maintained
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Predator-Prey interactions
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if predators form a "search image", then the predator keys on the most common prey giving a selective advantage to the rare prey
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Parasite-host interactions
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parasites may be selected to attack the most common host, and hosts may be selected to defend against the most common parasites.
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Mimicry systems example
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ex. venomous coral snakes and their non-venomous king snake mimics
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Fisher argued that the 50:50 sex ration observed in most animals is the result of
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frequency-dependent selection
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50:50 sex ratio
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if the primary sex ratio is skewed, parents that produce more of the rare sex have a fitness advantage because their offspring will have higher mating success; eventually most populations evolve mechanisms that stabilize the sex ratio
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Migration (gene flow)
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the movement of alleles among populations
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Migration is an ______ not to be confused with the seasonal movement of individuals
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evolutionary definition
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For there to be an evolutionary impact of migration,
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the movement must include subsequent incorporation of the migrants genes into the local gene pool (if an individual moves into a new population, but does not successfully breed, then there is no gene flow)
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migration will eventually
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equalize frequencies of two populations without any opposing force
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migration can cause
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allele frequencies of populations to change
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Migration can be powerful mechanisms for
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small populations receiving migrants from large source
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gene flow tends to
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homogenize allele frequencies
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Migration tends to prevent
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evolutionary divergence of populations
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Migration tends to counteract local adaptation, but
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may also introduce alleles with selective advantage
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Why do you see banded snakes on the islands?
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banded snakes migrating to the islands (tends to counter act local adaptation)
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Genetic Drift
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alteration of gene frequencies due to chance (stochastic) effects
-the result of finite population size (violates H-W assumption) |
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smaller the population,
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the greater genetic grift
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sampling error
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error caused by observing a sample instead of whole population
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Drift is
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differential reproductive success that is due to sampling error
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Selection is
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differential reproductive success that is due to a trait phenotype that confers higher fitness
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Founder effect
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change in allele frequency in newly founded population due to the colonization of a few founders (i.e., drift)
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Founder effect example: silvereye bird
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diversity less and less as moved from Tasmania to island, to next island, etc. (take handful from one to island #2. take handful from #2 to #3, etc.)
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Founder effect example: Pingelapese people
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20 survivors after typhoon and famine in 1775; one survivor had colorblindness= frequency is now 1 in 20 on the island compared to rest of the world which is 1 in 20,000
High frequency due to random chance, not selection. |
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Genetic drift causes
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the random fixation of alleles and loss of heterozygosity
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every population follows unique evolutionary path because
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drift is random
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drift in large populations vs. small populations
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more rapid and dramatic effect on allele frequencies (and thus heterozygosity) in small populations than in large populations
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Given enough time, drift can be
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important evolutionary mechanism even in large populations
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In the absence of any other evolutionary mechanism, an allele will become...
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fixed (frequency is 1) or lost (frequency is 0)
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probability that an allele becomes fixed is equal to
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its starting allele frequency
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heterozygosity is at maximum when
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p=q (=0.5 with 2 alleles)
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If deviate from 0.5
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have less heterozygosity
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If lose or fix an allele then heterozygosity
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is 0
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Effective population size (Ne)
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the number of individuals in an ideal population (in which every individual reproduces) in which the rate of genetic drift would be the same as it is in the actual population
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Why Ne<<Na (effective population size << actual census size)?
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because of non binomial variance in reproductive success (highly skewed reproductive success), skewed sex ratios, fluctuating population size
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the rate of genetic drift is highly influenced by
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the lowest population size in a series of generations
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the effective population size (Ne) over multiple generations is best represented by
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the harmonic mean not the arithmetic mean
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population bottleneck (or genetic bottleneck)
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an evolutionary event in which a significant percentage of a population or species is killed or otherwise prevented from reproducing.
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drift reduces genetic variation as the result of
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extinction of alleles
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drift generally does not produce a fit between organism and environment; can in fact, result in
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nonadaptive or maladaptive changes
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if s>>1/Ne
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selection predominates
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if s<<1/Ne
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then drift predominates
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Consequences of drift on the selection process
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-a population may not be exactly at the equilibrium expected under selection alone, because drift can move it away from the equilibrium
-selection is more efficient in larger populations -A population bottleneck can cause a deleterious allele to increase in frequency -Drift and selection in concert can move a population to a new equilibrium if there are multiple stable equilibria. Selection by itself cannot do this. |
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How can random genetic drift cause maladaptive evolution?
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-Since genetic drift can cause allele frequencies to increase, even deleterious alleles can be advanced and fixed in populations. The result is a decrease in mean population fitness.
-Small populations are especially prone to this effect. If s<<1/Ne |
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In a small population, the effects of drift will
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dominate the dynamics of allele frequency change from one generation to the next
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Because allele frequencies change by chance in finite populations, experiments must be designed to
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allow us to reject the hypothesis that drift has caused observed changes
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Small populations lose genetic diversity rapidly. Has two consequences:
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1. genetic diversity is the raw material for adaptive evolution (i.e., evolution via natural selection)
--Populations may lose ability to respond to changing environment 2. Loss of alleles entails increase in homozygosity which can expose deleterious alleles --This is similar to inbreeding, which we will cover next time. |
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mating systems
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the rules by which pairs of gametes are chosen from the local gene pool to be united in a zygote with respect to a particular locus or genetic system
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4 mating systems
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1. Random mating (H-W equilibrium)
2. Inbreeding (mating between biological relatives) 3. Assortative Mating (preferential mating between phenotypically similar individuals) 4. Disassortative Mating (preferential mating between phenotypically dissimilar individuals) (2,3,4 different forms of nonrandom mating) |
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Inbreeding
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mating between close relatives
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Two individuals are related if
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among the ancestors of the first individual are one or more ancestors of the second individual
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Inbreeding leads to deviations from H-W equilibrium by
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causing a deficit of heterozygotes- changes genotype frequencies
DOES NOT CHANGE ALLELE FREQUENCIES! |
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the inbreeding coefficient, F
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the probability that a randomly chosen individual carries two copies of an allele that are identical by descent from a recent ancestor
-the probability that an individual is autozygous |
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autozygous must be
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homozygous, but homozygous does not mean autozygous
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Heterozygosity after t generations of selfing
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Ht=(1/2)^t x H0
(as t increases, Ht decreases) |
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F
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the fraction of the population that is autozygous
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1-F
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the fraction that is allozygous
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observed heterozygosity always lowers with
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inbreeding
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As the inbreeding coefficient (F) increases, fitness often
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decreases
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As increase homozygosity,
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increase exposure of deleterious recessive alleles or reduction in heterozygote advantage
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inbreeding is caused by
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non random mating and leads to changes in genotype frequencies but not allele frequencies
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Random genetic drift
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occurs in finite populations even with completely random mating and leads to changes in both genotype and allele frequencies
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Both inbreeding and random genetic drift cause
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a decline in observed heterozygosity, but the mechanism is different in that drift results in the loss of alleles
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