Chapter 1-7 Flashcards
Coreceptor inhibitors.
These bar HIV from entering host cells in the first place by preventing them from latching onto the host cell’s CCR5 molecules.
Fusion inhibitors.
These bar HIV from entering host cells by interfering
with HIV’s gp120 or gp41 proteins.
Reverse transcriptase inhibitors.
Some, like AZT, inhibit reverse tran-
scriptase by mimicking the normal building blocks of DNA. Others inhibit
reverse transcriptase by interfering with the enzyme’s active site.
Integrase inhibitors.
These block HIV’s integrase from inserting HIV’s
DNA into the host genome, preventing the transcription of new viral RNAs.
Protease inhibitors.
These prevent HIV’s protease enzyme from cleaving
viral precursor proteins to produce mature components for new virions.
microevolution.
First, species are not immutable, but change through
time. In a population of birds, for example, the average beak size may change from
one generation to the next.
speciation.
lineages
split and diverge, thereby increasing the number of species.
macroevolution.
over long periods of time, novel forms of life can derive from
earlier forms. Tetrapods, for example, arose from a lineage of fish.
vestigial structures.
A vestigial structure is a useless or rudimentary version of a body part that has an
important function in other, closely allied, species.
fossil
any trace of an organism that lived in the past.
fossil record.
The worldwide collection
of fossils
law of succession.
The general pattern of
correspondence between fossil and living forms from the same locale
transitional forms,
A species that exhibits
traits common to ancestral and derived groups,
especially when the groups are sharply differentiated.
processed pseudogenes.
A pseudogene that
originated when a messenger RNA from which
the introns had already been removed was reverse-transcribed and inserted into the genome.
exons
A nucleotide sequence that occurs between introns and that remains in the messenger
RNA after the introns have been spliced out.
intron
A noncoding stretch of DNA nucleotides that occurs
between the coding regions of a gene and that
must be spliced out after transcription to produce a functional messenger RNA.
retrotransposon
Transposable elements
that move via an RNA intermediate and contain the coding sequence for reverse transcriptase; closely related to retroviruses.
uniformitarianism
The assumption (some-
times called a “law”) that processes identical to those at work today are responsible for events that occurred in the past; first articulated by James Hutton, the founder of modern geology.
natural selection
A difference, on average,
between the survival or fecundity of individuals with certain phenoypes compared with individuals with other phenotypes.
Darwinian fitness
The extent to which an
individual contributes genes to future generations, or an individual’s score on a measure of performance expected to correlate with genetic contribution to future generations (such as life-time reproductive success).
adaptation
A trait that increases the ability of
an individual to survive or reproduce compared
with individuals without the trait.
adaptive
Describes a trait that increases the
fitness of an individual relative to that of individuals lacking the trait.
heritability
In the broad sense, that fraction
of the total phenotypic variation in a population that is caused by genetic differences among individuals; in the narrow sense, that fraction of the total variation that is due to the additive effects of genes.
evolutionary tree
A diagram (typically an
estimate) of the relationships of ancestry and descent among a group of species or populations; in paleontological studies the ancestors may be known from fossils, whereas in studies of extant species the ancestors may be hypothetical constructs. Also called a phylogenetic tree or phylogeny.
root
The location on a phylogeny of the
common ancestor of a clade.
transitions
In DNA, a mutation that substitutes a purine for a purine or a pyrimidine for a pyrimidine.
evolutionary relationships
Patterns of genealogical kinship among species resulting from
descent with modification from common ancestors. Species A and B are more closely related to each other than either is to C if A and B share a more recent common ancestor than either shares with C.
sister species
The species that diverged from
the same ancestral node on a phylogenetic tree.
derived characters
A character present in
one or more species in a clade that was not present in the clade’s common ancestor; an evolutionary novelty; also known as an apomorphy; used in contrast with ancestral character.
apomorphy
A character present in one or
more species in a clade that was not present in the clade’s common ancestor; an evolutionary novelty. Also known as a derived character.
plesiomorphy
An ancestral character; that is,
a character present in the common ancestor of a clade.
synapomorphy
A shared, derived character;
in a phylogenetic analysis, synapomorphies are used to define clades and distinguish them from
outgroups.
monophyletic group
The set of species (or populations) descended from a common ancestor.
paraphyletic group
A set of species that includes a common ancestor and some, but not all, of its descendants.
polyphyletic group
A set of species that are
grouped by similarity, but not descended from a common ancestor.
polytomy
A node, or branch point, on a phylogeny with more than two descendant lineages emerging.
Outgroup
A taxonomic group that diverged
prior to the rest of the taxa in a phylogenetic analysis.
parsimony
A criterion for selecting among
alternative patterns or explanations based on minimizing the total amount of change or complexity.
uninformative characters
A character that
fails to help distinguish among the possible trees in a parsimony analysis because its distribution requires the same number of evolutionary changes on all of them.
convergent evolution
The independent appearance in different lineages of similar derived characters
reversal.
The loss of derived traits in a lineage, resulting in
a return to the ancestral condition
homoplasy.
Similarity in character states due to convergence and/or reversal
likelihood
The probability of a particular outcome given a model of the process that produced it. For example we might calculate the probability that a pair of parents will have an offspring with a particular multilocus genotype given a model specifying how closely the loci in question are linked. Or we might calculate the probability of getting a particular set of sequences given a phylogeny of the species from which we sampled them.
bootstrapping
In phylogeny reconstruction,
a technique for estimating the strength of the evidence in our data for the existence of a particular clade. Involves analyzing replicate data
sets constructed by sampling, with replacement, from our actual data. Bootstrap support for a clade runs from 0 to 100, with higher values
indicating stronger support.
posterior probability
In Bayesian statistical inference, the probability of the hypothesis given the data. Calculated from the probability
of the data given the hypothesis, the prior probability of the hypothesis, and the prior probability of the data.
prior probability
In Bayesian statistical inference, the probability assigned to a hypothesis before considering the data.
Bayesian phylogeny inference
An approach to phylogeny inference based on computing the probability that a particular tree is correct, given a specific model of evolution for the characters being analyzed and the data observed.
clade credibility
In Bayesian phylogeny inference, the sum of the posterior probabilities of all the possible phylogenies in which a clade appears. Less precisely, the probability, given the data, that a hypothesized clade is real.
SINEs
Short interspersed elements—a group
of non-reverse-transcriptase-encoding retrotransposons.
LINEs
Long interspersed elements—a group of reverse-transcriptase-encoding retrotransposons common in the genomes of eukaryotes.
molecular clock
The hypothesis that base
substitutions accumulate in populations in a clock-like fashion; that is, as a linear function of time.
neutral
A mutation that has no effect on the fitness of the bearer.
biogeography
The study of where organisms live and how they got there.
phylogeography
The use of evolutionary trees in answering questions about the geographic distribution of organisms.
genetic variation
Differences among individuals in a population that are due to differences in genotype.
environmental variation
Differences among individuals in a population that are due to differences in the environments they have experienced.
genotype-by-environment interaction
Differences in the effect of the environment on the phenotype displayed by different genotypes; for example, among people living in the same location some change their skin color with the seasons and others do not.
alleles
Variant forms of a gene, or variant nucleotide sequences at a particular locus.
genotype
The combination of alleles an individual carries at one or more loci of interest.
phenotype
The set of traits an individual exhibits.
inducible defense
A character that is adaptive because of its role in evading predation and that develops only in the presence of a cue emanating from the predator.
expression
In molecular biology, the production, from the information encoded in a gene, of a functional protein or RNA.
reaction norm
The pattern of phenotypes an individual may develop upon exposure to different environments
phenotypic plasticity
Variation, under environmental influence, in the phenotype associated with a genotype.
mutations
Changes in the genome range in size from substitutions of one base for another to gains and losses of
chromosomes.
premutations
Alterations in a DNA sequence, due to chemical degradation and replication errors, that may still potentially be detected and repaired.
point mutation
Alteration of a single base in
a DNA sequence.
transition
Substitution of a purine for a
purine or a pyrimidine for a pyrimidine
transversion
In DNA, a mutation that substitutes a purine for a pyrimidine, or a pyrimidine for a purine.
synonymous substitution
A DNA substitution that does not change the amino acid or RNA sequence specified by the gene. Also
called a silent (or silent-site) substitution.
nonsynonymous substitution
A DNA substitution that changes the amino acid sequence specified by a gene.
nonsense mutation
A mutation creating a new stop codon in the coding region of a gene.
indels
A type of mutation based on the insertion or deletion of one or more deoxyribonucleotides (bases).
gene duplication
Generation of an extra copy of a locus, usually via unequal crossing over or retroposition.
unequal crossing over
an error in the genetic recombination that happens during meiosis.
paralogous
Duplicated genes found in the
same genome; describes the relationship among members of the same gene family. A type of genetic homology.
orthologous
Genes that diverged after a speciation event; describes the relationship among homologous genes found in different species.
inversions
A region of DNA that has been
flipped, so that the genes are in reverse order; results in lower rates of crossing-over and thus tighter linkage among loci within the inversion.
linkage
The tendency for alleles at different
loci on a chromosome to be inherited together. Also called genetic linkage.
polymorphic
Describes a population, locus, or trait for which there is more than one phenotype or allele; variable.
cline
This type of regular change in the frequency of an allele or an inversion over a geographic area
mutation accumulation
Describes an experiment in which lineages of organisms are insulated as much as possible from natural selection, and are thus allowed to accumulate mutations by genetic drift. Also describes a hypothesis for the evolution of senescence in which
late-acting deleterious mutations accumulate because they are unoppossed by selection.
Population genetics
The branch of evolutionary biology responsible for investigating processes that cause changes in allele and genotype frequencies in populations.
population
is a group of interbreeding individuals and their offspring.
gene pool
The set of all copies of all alleles in
a population that could potentially be contributed by the members of one generation to the members of the next generation.
genetic drift
Change in the frequencies of
alleles in a population resulting from sampling error in drawing gametes from the gene pool to make zygotes and from chance variation in the survival and/or reproductive success of individuals; results in nonadaptive evolution.
Hardy–Weinberg Equilibrium Principle
- There is no selection.
- There is no mutation.
- There is no migration.
- There are no chance events
- Individuals choose their mates at random.
selection
Synonym for natural selection.
heterozygote superiority (overdominance.)
Describes a situation in which heterozygotes at a particular locus tend to have higher fitness than homozygotes.
mutation–selection balance
Describes an equilibrium in the frequency of an allele that occurs because new copies of the allele are created by mutation at exactly the same rate that old copies of the allele are eliminated by natural selection.
