Evolution Exam 1

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HIV

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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.

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Reverse transcriptase

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RNA is transcripted into DNA for replication

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evolution

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genetic change in a group of organisms

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essentialism

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organism is an imperfect representation of the ideal perfect form

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Linnaeus

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Systema Naturae- basis of modern classification; Developed hierarchical classification system

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uniformitarianism

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uniform processes
Charles Lyell and James Hutton
nature changes
world very old

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Lamarck

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developed early evolutionary theory
Mechanisms of evolution: 1. Use and disuse 2. Believed in inheritance of acquired characteristics 3. organisms evolved in specific direction

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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)

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Malthus

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Economist; wrote essay on population growth and resources that influenced Darwin (1838)

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Alfred Russel Wallace

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Developed natural selection concept separately from Darwin; sent it to Darwin to look over (1858); ideas of Darwin and _______ presented together

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neo-Lamarckism

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Post Darwinian return to the evolutionary theory of Lamarck.

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orthogenesis

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Post Darwinian idea that evolution occurs in a specific generation

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mutationalism

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Post Darwinian idea that evolution brought about by mutations that have major effects

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modern synthesis

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(1930s & 1940s) resulted in the synthesis of Darwinian evolution and Mendelian genetics as the mechanism for natural selection

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natural selection

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Differential reproduction of genotypes; Only evolutionary force that leads to adaptation

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Lamarck

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developed early evolutionary theory
Mechanisms of evolution: 1. Use and disuse 2. Believed in inheritance of acquired characteristics 3. organisms evolved in specific direction

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fitness

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relative reproductive success of a genotype

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scientific theory

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widely held explanation supported by much evidence

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evolutionary theory

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widely held idea that explains much of biological diversity and many life processes

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homology

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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

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anagenesis

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evolution within a lineage (line of descent)

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cladogenesis

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branching of a lineage

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phylogeny

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evolutionary relationships among group of organisms

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phylogenetic analysis

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study of phylongeny

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phylogenetic tree

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graphical representation of evolutionary relationship

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OTUs (Operational Tacanomic Units)

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Organismal or biological units for which phylogeny is created

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terminal node

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represents OTUs

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internal node

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represents common ancestors; usually extinct

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branch

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evolutionary connections

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outgroup

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used to root the tree (a rooted tree has a common ancestor to all OTUs)

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ingroup

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monophyletic set of species whose relationships we wish to infer.

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gene tree

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diagram representing the history by which gene copies have been derived from ancestral gene copies in previous generations

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character

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characteriestic or trait

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taxon

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named taxonomic unit to which an individual or groups of individuals belong

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topology

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branching pattern of the tree

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monophyletic taxon

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set of all known descendants from a single ancestor

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polyphyletic taxon

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group of organisms that are not all descendants from a single ancestor

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paraphyletic taxon

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group of orgnaisms that includes some but not all descendants of a single ancestor

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plesiomorphy

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terminal node has the same trait as the ancestor (primitive trait)

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apomorphy

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terminal node has a trait different from that of the ancestor (derived trait)

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autopomorphy

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unique characteristic

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synapomorphy

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shared derived characters

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rooted tree

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has a common ancestor to all OTUs

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parsimony

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preffered explanation is the simplest one

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homoplasy

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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.

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convergent evolution

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natural selection causes traits with different evolutionary orgins to be similar

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evolutionary reversal

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trait that has been changed reverts back to ancestral form

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parallel evolution

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the evolution of similar of identical features independently in related lineages, though usually to be based on similar modifications of the same developmental pathways

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phenetic

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Distance measures based on overall differneces in sequence

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cladistics

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Parsimony methods based on minimum number of evolutionarey steps used to produce a sequence of OTUs

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mosaic evolution

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evolution of different characters within a lineage or clade at different rates, more or less independently of one another

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gradualism

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proposition that large differences in phenotypic characters have evolved through many slightly different intermediate states

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heterochrony

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An evolutionary change in phenotype caused by an alteration of timing of developmental events

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paedomorphism (neoteny)

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possession in the adult stage of features typical of the juvenile stage of the organism's ancestor.

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allometric growth

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Growth of a feature during ontogeny at a rate different from that of another feature with which it is compared

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igneous rocks

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formed from molten material (magma); don't contain fossils

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sedimentary rocks

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formed from sediments; contain fossils

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metamorphic rocks

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formed through alteration of igneous of sedimentary rock; any fossils usually destrpyed through _________ process

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plate tectonics

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Outer layer of Earth composed of plated that move; surface of the Earth has undergone change; present positions of continents different from past positions

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fossil

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any trace of an organism that lived in the past

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fossil record

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worldwide collection of fossils in the world

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compression and impression fossils

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structure buried by sediments; leaves impression on material below

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replacement fossils

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structure buried in sediments, dissolved minerals replace original material;

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permineralization

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mineralized water seeps into pores and menerals precipitate into spaces

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cast fossil

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structure decays or shells dissolve after being buried in sediments; new material fills space and hardens to rock

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mold fossil

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structure decays or shells dissolve after being buried in sediments; space unfilled

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unaltered remains

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may be preserved in special environments (i.e. ice, peat bogs, amber)

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mutation

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heritable change in DNA

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somatic mutation

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mutations in somatic cells; don't pass to offspring

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germline mutation

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mutation in germ line cells

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gene mutation

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mutation affecting a single gene

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chromosome mutation

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change in the number or structure of chromosomes

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transition

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a mutation that changes a nucleotide to another nucleotide in the same class

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transversion

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A mutation that changes a nucleotide to another nucleotide in the opposite class

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missense mutation

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alters amino acids in protein

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nonsense mutation

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alters a sense codon to a stop codon

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silent mutation

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Doesn't alter amino acid sequence due to synonymous codons and noncoding DNA

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neutral mutation

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Alters the amino acid structure but doesn't affect the function of the protein

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gene deletion

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removal of a gene from the chromosome due to unequal crossing over or strand slippage

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expanding trinucleotide repeat

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the number of copies of trinucleotides increase most likely due to slippage during replication; occurs in Huntington disease.

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transposable element

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genetic elements that can move; includes: insertion sequences, DNA transposons, and retrotransposons

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retrotransposon

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similar to a retrovirus; carry a gene for enzyme reverse transcriptase

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chromosome rearrangement

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change in the chromosome structure

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aneuploidy

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change in the number of individual chromosomes

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polyploidy

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change in the number of chromosome sets

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chromosome duplication

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the addition of an extra copy of a chromosome in the genome

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chromosome deletion

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the removal of an entire chromosome in the genome

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chromosome inversion

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A 180 degree reversal of the orientation of a part of a chromosome, relative to some standard chromosome.

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chromosome translocation

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by breakage and union, two nonhomologous chromosomes exchange segments

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dosage effects

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The number of doses of a protein has an effect on the phenotype of the organism.

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monosomic

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2n-1; missing a chromosome

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nullisomic

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2n-2; missing a homologous chromosome pair

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trisomic

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2n+1; having an extra chromosome

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tetrasomic

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2n+2; having 2 extra chromosomes

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autopolyploidy

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a type of polyploidy in which all genomes are from a single species

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allopolyploidy

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A type of polyploidy in which the genomes are from 2 or more species

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Mendelian population

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A diploid, sexually reprodiucing group of individuals

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allelic frequency

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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

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genotypic frequency

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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

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Hardy-Weinberg law

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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

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Hardy-Weinberg equilibrium

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a population at the following genotypic proportions p2+2pq+q2

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random mating

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mating without regard to genotype; the probability of mating between genotypes is equal to the product of the genotype frequencies.

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positive assortative mating

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tendency for like individuals to mate

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negative assortative mating

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tendency for unlike individuals to mate

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inbreeding

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preferential mating between related individuals which causes a departure from the Hardy-Weinberg equilibrium

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inbreeding coefficient

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F; measures inbreeding in a population

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bone morphogenic protein 4

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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

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inbreeding depression

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inbreeding increases the frequency of homozygotes for deleterious allels; decreases fitness

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genetic drift

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changes in allelic frequency due to chance factors; changes due to sampling error (chance deviations from expected ratios)

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amphibians

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includes frogs, salamanders, and caecilians

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Edwards Plateau

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region of central TX characterized by cretaceous limestone;

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Edwards aquifer

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springs and caves inhabited by endemic aquatic organisms

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Eurycea

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Salamanders

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founder effect

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population founded by a small number of individuals; initial gene pool consists of a limited number of alleles; often seen on island populations

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bottleneck effect

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population size reduced; afterwards, population is reestablished from a limited gene pool

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effective population size

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effective number of breeding adults

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fixation

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attainment of a frequency of 1 (100%) by an allele in a population, which becomes monomorphic for the allele

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nodes

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branching events in a phylogenic tree

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molecular clock

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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

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haplotypes

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a DNA sequencethat differs from homologous sequences at one or more base pair sites

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polytomy

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A node with three or more branches representing a group of three or more taxa whose relationships cannot be confidently resolved

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horizontal gene transfer

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Movement of genes between individual organisms other than by transmission from parents to their offspring.

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cladogram

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A branching diagram depicting relationships among taxa; an estimated history of the relative sequence in which they have evolved from common ancestors

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clade

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The set of species descended from a particular ancestral species

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evolutionary trend

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succession of changes of a character in the same direction, either within a single lineage or in many lineages independently

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geological time scale

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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

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radiometric dating

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determination of the absolute ages of geological events by measuring the decay of certain radioactive elements in minerals that form in igneous rock

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strata

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layers of sediment deposited at different times

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eras, periods, and epochs

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divisions of the geological time scale

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Dollo's law

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complex characters once lost are not regained

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Cope's rule

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evolutionary trend of body size to increase over time in many animal clades

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grade

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Multiple lineages that have evolved through similar stages

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punctuated equilibria

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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

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phyletic gradualism

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the traditional notion of slow, incremental change in evolution

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intron

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A part of a gene that is not translated into a polypeptide

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codon

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a triplet of bases in mRNA that specifies a particular amino acid in the growing polypeptide chain

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microsatellite

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A short, highly repeated, untranslated DNA sequence

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gene family

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groups of genes that are similar in sequence and often have related functions

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gene control region

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untranscribed sequences to which regulatory proteins produced by other genes bind

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pseudogene

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A nonfunctional member of a gene family that has been derived from a functional gene

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allele

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One of several forms of the same gene, presumably differing by mutation of the DNA sequence; usually recognized by phenotypic effects

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genetic marker

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detectable mutations that geneticists use to recognize specific regions of chromosomes or genes

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frameshift mutation

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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

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synonymous mutation

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Fication of a base pair change that does not alter the amino acid in the protein product of the gene; also silent substitution

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nonsynonymous mutation

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A base pair substitution in DNA that results in an amino acid substitution in the protein product; also replacement substitution

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unequal crossing over

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unequal exchange of DNA that can occur between two homologous sequences or chromosomes that are not perfectly aligned

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back mutation

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mutaton of a mutant allele back to the allele (usually the wild type) from which it arose

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polygenic character

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A character whose variation is based wholly or in part on allelic variation at more than a few loci

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homeotic mutation

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A mutation that causes a transformation of one structure into another of the organism's structures

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pleiotropy

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A phenotypic effect of a gene on more than one character

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panmixia

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Random mating among members of a population

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concealed genetic variation

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genetic variation that occurs in a recessive allele

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polymorphism

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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

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monomorphic

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having one form; refers to a population in which virtually all individuals have the same genotype at a locus

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lethal allele

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An allele (usually recessive)that causes virtually complete mortality, usually early in development

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allozyme

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One of several forms of an enzyme encoded by different alleles at a locus

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linkage disequilibrium

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The associaton of two alleles at two or more loci more frequently (or less frequently) than predicted by their individual frequencies

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linkage equilibrium

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The association of two alleles at two or more loci at the frequency predicted by their individual frequencies

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sympatric

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of two species or populations, occupying the same geographic locality so that the opportunity to interbreed is presented

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allopatric

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Of a population or species, occupying a geographic region different from that of another population or species

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parapatric

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Of two species or populations, having contigous but non-overlapping geographic distributions

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subspecies

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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

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hybrid zone

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A region in which genetically distinct populations come into contact and produce at least some offspring of mixed ancestry

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cline

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A gradual change in an allele frequency or in the mean of a character over a geographic transect

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ecotype

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A genetically determined phenotype of a species that is found as a local variant associated with certain ecological conditions

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character displacement

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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

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genetic distance

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Any of several measures of the degree of genetic difference between populations, based on differences in allel frequencies

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sampling error

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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

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coalescence

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Derivation of the gene copies in one or more populations from a single ancestral copy, viewed retrospectively (from the present back into the past)

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neutral theory of molecular evolution

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hypothesis that states that the evolution of DNA sequences occurs by genetic drift rather than by natural selection