Evolution Exam 1
Terms
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- HIV
-
human immunodeficiency virus
RNA retrovirus that uses reverse transciptase to replicate; has envelope around it taken from host cell; rapid rate of evolution due to high mutation rate caused by errors in action of reverse transcriptase. - Reverse transcriptase
- RNA is transcripted into DNA for replication
- evolution
- genetic change in a group of organisms
- essentialism
- organism is an imperfect representation of the ideal perfect form
- Linnaeus
- Systema Naturae- basis of modern classification; Developed hierarchical classification system
- uniformitarianism
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uniform processes
Charles Lyell and James Hutton
nature changes
world very old - Lamarck
-
developed early evolutionary theory
Mechanisms of evolution: 1. Use and disuse 2. Believed in inheritance of acquired characteristics 3. organisms evolved in specific direction - Darwin
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came from wealthy family; studied medicine and theology
Naturalist on voyage of Beagle
Developed theory of natural selection; amassed evidenc but didn't publish; Wrote the orgin of species (1859) - Malthus
- Economist; wrote essay on population growth and resources that influenced Darwin (1838)
- Alfred Russel Wallace
- Developed natural selection concept separately from Darwin; sent it to Darwin to look over (1858); ideas of Darwin and _______ presented together
- neo-Lamarckism
- Post Darwinian return to the evolutionary theory of Lamarck.
- orthogenesis
- Post Darwinian idea that evolution occurs in a specific generation
- mutationalism
- Post Darwinian idea that evolution brought about by mutations that have major effects
- modern synthesis
- (1930s & 1940s) resulted in the synthesis of Darwinian evolution and Mendelian genetics as the mechanism for natural selection
- natural selection
- Differential reproduction of genotypes; Only evolutionary force that leads to adaptation
- fitness
- relative reproductive success of a genotype
- scientific theory
- widely held explanation supported by much evidence
- evolutionary theory
- widely held idea that explains much of biological diversity and many life processes
- homology
- Possession by 2 or more species of a character state derived, with or without modivication, from their common ancestor; homologous traits have common evolutionary orgin
- anagenesis
- evolution within a lineage (line of descent)
- cladogenesis
- branching of a lineage
- phylogeny
- evolutionary relationships among group of organisms
- phylogenetic analysis
- study of phylongeny
- phylogenetic tree
- graphical representation of evolutionary relationship
- OTUs (Operational Tacanomic Units)
- Organismal or biological units for which phylogeny is created
- terminal node
- represents OTUs
- internal node
- represents common ancestors; usually extinct
- branch
- evolutionary connections
- outgroup
- used to root the tree (a rooted tree has a common ancestor to all OTUs)
- ingroup
- monophyletic set of species whose relationships we wish to infer.
- gene tree
- diagram representing the history by which gene copies have been derived from ancestral gene copies in previous generations
- character
- characteriestic or trait
- taxon
- named taxonomic unit to which an individual or groups of individuals belong
- topology
- branching pattern of the tree
- monophyletic taxon
- set of all known descendants from a single ancestor
- polyphyletic taxon
- group of organisms that are not all descendants from a single ancestor
- paraphyletic taxon
- group of orgnaisms that includes some but not all descendants of a single ancestor
- plesiomorphy
- terminal node has the same trait as the ancestor (primitive trait)
- apomorphy
- terminal node has a trait different from that of the ancestor (derived trait)
- autopomorphy
- unique characteristic
- synapomorphy
- shared derived characters
- rooted tree
- has a common ancestor to all OTUs
- parsimony
- preffered explanation is the simplest one
- homoplasy
- Possession by 2 or more species of a similar or identical character state that has not been derived by both speices from their common ancestor.
- convergent evolution
- natural selection causes traits with different evolutionary orgins to be similar
- evolutionary reversal
- trait that has been changed reverts back to ancestral form
- parallel evolution
- the evolution of similar of identical features independently in related lineages, though usually to be based on similar modifications of the same developmental pathways
- phenetic
- Distance measures based on overall differneces in sequence
- cladistics
- Parsimony methods based on minimum number of evolutionarey steps used to produce a sequence of OTUs
- mosaic evolution
- evolution of different characters within a lineage or clade at different rates, more or less independently of one another
- gradualism
- proposition that large differences in phenotypic characters have evolved through many slightly different intermediate states
- heterochrony
- An evolutionary change in phenotype caused by an alteration of timing of developmental events
- paedomorphism (neoteny)
- possession in the adult stage of features typical of the juvenile stage of the organism's ancestor.
- allometric growth
- Growth of a feature during ontogeny at a rate different from that of another feature with which it is compared
- igneous rocks
- formed from molten material (magma); don't contain fossils
- sedimentary rocks
- formed from sediments; contain fossils
- metamorphic rocks
- formed through alteration of igneous of sedimentary rock; any fossils usually destrpyed through _________ process
- plate tectonics
- Outer layer of Earth composed of plated that move; surface of the Earth has undergone change; present positions of continents different from past positions
- fossil
- any trace of an organism that lived in the past
- fossil record
- worldwide collection of fossils in the world
- compression and impression fossils
- structure buried by sediments; leaves impression on material below
- replacement fossils
- structure buried in sediments, dissolved minerals replace original material;
- permineralization
- mineralized water seeps into pores and menerals precipitate into spaces
- cast fossil
- structure decays or shells dissolve after being buried in sediments; new material fills space and hardens to rock
- mold fossil
- structure decays or shells dissolve after being buried in sediments; space unfilled
- unaltered remains
- may be preserved in special environments (i.e. ice, peat bogs, amber)
- mutation
- heritable change in DNA
- somatic mutation
- mutations in somatic cells; don't pass to offspring
- germline mutation
- mutation in germ line cells
- gene mutation
- mutation affecting a single gene
- chromosome mutation
- change in the number or structure of chromosomes
- transition
- a mutation that changes a nucleotide to another nucleotide in the same class
- transversion
- A mutation that changes a nucleotide to another nucleotide in the opposite class
- missense mutation
- alters amino acids in protein
- nonsense mutation
- alters a sense codon to a stop codon
- silent mutation
- Doesn't alter amino acid sequence due to synonymous codons and noncoding DNA
- neutral mutation
- Alters the amino acid structure but doesn't affect the function of the protein
- gene deletion
- removal of a gene from the chromosome due to unequal crossing over or strand slippage
- expanding trinucleotide repeat
- the number of copies of trinucleotides increase most likely due to slippage during replication; occurs in Huntington disease.
- transposable element
- genetic elements that can move; includes: insertion sequences, DNA transposons, and retrotransposons
- retrotransposon
- similar to a retrovirus; carry a gene for enzyme reverse transcriptase
- chromosome rearrangement
- change in the chromosome structure
- aneuploidy
- change in the number of individual chromosomes
- polyploidy
- change in the number of chromosome sets
- chromosome duplication
- the addition of an extra copy of a chromosome in the genome
- chromosome deletion
- the removal of an entire chromosome in the genome
- chromosome inversion
- A 180 degree reversal of the orientation of a part of a chromosome, relative to some standard chromosome.
- chromosome translocation
- by breakage and union, two nonhomologous chromosomes exchange segments
- dosage effects
- The number of doses of a protein has an effect on the phenotype of the organism.
- monosomic
- 2n-1; missing a chromosome
- nullisomic
- 2n-2; missing a homologous chromosome pair
- trisomic
- 2n+1; having an extra chromosome
- tetrasomic
- 2n+2; having 2 extra chromosomes
- autopolyploidy
- a type of polyploidy in which all genomes are from a single species
- allopolyploidy
- A type of polyploidy in which the genomes are from 2 or more species
- Mendelian population
- A diploid, sexually reprodiucing group of individuals
- allelic frequency
- The proportion of gene copies in a population that are a given allele; the probability of finding this allele when a gene is taken randomly from the population; also gene frequency
- genotypic frequency
- The proportion of genotypes in a population that are a given genotype; the probability of finding this genotype when a gene is taken randomly form the population
- Hardy-Weinberg law
- Indicates what happens when only reproduction occurs; In a large randomly mating population free from evolutionary forces the allelic frequency does not change and the genotypic frequency stabalizes after one generation in the proportion p2+2pq+q2; applies only to a single locus
- Hardy-Weinberg equilibrium
- a population at the following genotypic proportions p2+2pq+q2
- random mating
- mating without regard to genotype; the probability of mating between genotypes is equal to the product of the genotype frequencies.
- positive assortative mating
- tendency for like individuals to mate
- negative assortative mating
- tendency for unlike individuals to mate
- inbreeding
- preferential mating between related individuals which causes a departure from the Hardy-Weinberg equilibrium
- inbreeding coefficient
- F; measures inbreeding in a population
- bone morphogenic protein 4
- Bmp4 gene which is importnat in cranial and beak development in birds; increased expression of the gene results in longer, wider, and deeper beaks whereas decreased expression of the gene results in smaller beaks
- inbreeding depression
- inbreeding increases the frequency of homozygotes for deleterious allels; decreases fitness
- genetic drift
- changes in allelic frequency due to chance factors; changes due to sampling error (chance deviations from expected ratios)
- amphibians
- includes frogs, salamanders, and caecilians
- Edwards Plateau
- region of central TX characterized by cretaceous limestone;
- Edwards aquifer
- springs and caves inhabited by endemic aquatic organisms
- Eurycea
- Salamanders
- founder effect
- population founded by a small number of individuals; initial gene pool consists of a limited number of alleles; often seen on island populations
- bottleneck effect
- population size reduced; afterwards, population is reestablished from a limited gene pool
- effective population size
- effective number of breeding adults
- fixation
- attainment of a frequency of 1 (100%) by an allele in a population, which becomes monomorphic for the allele
- nodes
- branching events in a phylogenic tree
- molecular clock
- the concept of a steady rate of change in DNA sequences over time, providing a basis for dating the time of divergence of lineages if the rate of change cna be estimated
- haplotypes
- a DNA sequencethat differs from homologous sequences at one or more base pair sites
- polytomy
- A node with three or more branches representing a group of three or more taxa whose relationships cannot be confidently resolved
- horizontal gene transfer
- Movement of genes between individual organisms other than by transmission from parents to their offspring.
- cladogram
- A branching diagram depicting relationships among taxa; an estimated history of the relative sequence in which they have evolved from common ancestors
- clade
- The set of species descended from a particular ancestral species
- evolutionary trend
- succession of changes of a character in the same direction, either within a single lineage or in many lineages independently
- geological time scale
- geological eras and periods distinguished by distinctive fossil taxa; great changes in faunal composition due to mass extinctions mark many of the boundaries between them
- radiometric dating
- determination of the absolute ages of geological events by measuring the decay of certain radioactive elements in minerals that form in igneous rock
- strata
- layers of sediment deposited at different times
- eras, periods, and epochs
- divisions of the geological time scale
- Dollo's law
- complex characters once lost are not regained
- Cope's rule
- evolutionary trend of body size to increase over time in many animal clades
- grade
- Multiple lineages that have evolved through similar stages
- punctuated equilibria
- A pattern of rapid evolutionary change in the phenotype of a lineage separated by long periods of little change; also, a hypothesis intended to explain such a pattern, whereby phenotypic change transpires rapidly in small populations, in concert with the evolution of reproductive isolation
- phyletic gradualism
- the traditional notion of slow, incremental change in evolution
- intron
- A part of a gene that is not translated into a polypeptide
- codon
- a triplet of bases in mRNA that specifies a particular amino acid in the growing polypeptide chain
- microsatellite
- A short, highly repeated, untranslated DNA sequence
- gene family
- groups of genes that are similar in sequence and often have related functions
- gene control region
- untranscribed sequences to which regulatory proteins produced by other genes bind
- pseudogene
- A nonfunctional member of a gene family that has been derived from a functional gene
- allele
- One of several forms of the same gene, presumably differing by mutation of the DNA sequence; usually recognized by phenotypic effects
- genetic marker
- detectable mutations that geneticists use to recognize specific regions of chromosomes or genes
- frameshift mutation
- An insertion or deletion of base pairs in a translatedDNA sequence that alters the reading frame, resulting in multiple downstream changes in the gene product
- synonymous mutation
- Fication of a base pair change that does not alter the amino acid in the protein product of the gene; also silent substitution
- nonsynonymous mutation
- A base pair substitution in DNA that results in an amino acid substitution in the protein product; also replacement substitution
- unequal crossing over
- unequal exchange of DNA that can occur between two homologous sequences or chromosomes that are not perfectly aligned
- back mutation
- mutaton of a mutant allele back to the allele (usually the wild type) from which it arose
- polygenic character
- A character whose variation is based wholly or in part on allelic variation at more than a few loci
- homeotic mutation
- A mutation that causes a transformation of one structure into another of the organism's structures
- pleiotropy
- A phenotypic effect of a gene on more than one character
- panmixia
- Random mating among members of a population
- concealed genetic variation
- genetic variation that occurs in a recessive allele
- polymorphism
- The existence within a population of 2 or more genotypes, the rarest of which exceeds some arbitrarily low frequency; more rarely, the existence of phenotypic variation within a population, whether or not genetically based
- monomorphic
- having one form; refers to a population in which virtually all individuals have the same genotype at a locus
- lethal allele
- An allele (usually recessive)that causes virtually complete mortality, usually early in development
- allozyme
- One of several forms of an enzyme encoded by different alleles at a locus
- linkage disequilibrium
- The associaton of two alleles at two or more loci more frequently (or less frequently) than predicted by their individual frequencies
- linkage equilibrium
- The association of two alleles at two or more loci at the frequency predicted by their individual frequencies
- sympatric
- of two species or populations, occupying the same geographic locality so that the opportunity to interbreed is presented
- allopatric
- Of a population or species, occupying a geographic region different from that of another population or species
- parapatric
- Of two species or populations, having contigous but non-overlapping geographic distributions
- subspecies
- A named geographic race; a set of populations of a species that share one or more distinctive features and occupy a different geographic area from other subspecies
- hybrid zone
- A region in which genetically distinct populations come into contact and produce at least some offspring of mixed ancestry
- cline
- A gradual change in an allele frequency or in the mean of a character over a geographic transect
- ecotype
- A genetically determined phenotype of a species that is found as a local variant associated with certain ecological conditions
- character displacement
- Usually refers to a pattern of geographic variation in which a character differs more greatly between sympatric than between allopatric populations of two species; sometimes used for the evolutionary process of accentuation of differences between sympatric popuations of two species a s a result of the reproductive or ecolotical interactions between them
- genetic distance
- Any of several measures of the degree of genetic difference between populations, based on differences in allel frequencies
- sampling error
- the proportions of different kinds of alleles in a sample are likely to differ, by chance, from the proportions in the set of items from whcih the sample is drawn
- coalescence
- Derivation of the gene copies in one or more populations from a single ancestral copy, viewed retrospectively (from the present back into the past)
- neutral theory of molecular evolution
- hypothesis that states that the evolution of DNA sequences occurs by genetic drift rather than by natural selection