BIO 1B - Evolution

Phenotype

term to describe appearance of a trait; any aspect in the appearance/behavior of an organism

genotype

genetic makeup of an organism, term used to describe the alleles

struggle for existence

competition among members of a species for food, space, etc; brought about by over-reproduction where there are more offspring than can survive

hereditary/inheritance

the transmission of traits from one generation to the next via passing on of genes/DNA; important/crucial part of the evolutionary process

natural selection

key mechanism of evolution that causes species to change/diverge over time. differential survival and reproduction rates of individuals based upon their inherited traits; organisms w/ traits more adapted to their environment are more likely to survive and reproduce; only force of evolution that results in adaptation

evolution

repeated rounds of the filtering of development by ecology; process driven by over-reproduction that develops and diversifies different kinds of living organisms from earlier forms; transformation of species over time (descent w/ modification)

variation

arises through development and mutation, random in that it doesn't anticipate the needs of the organism but not random w/ respect to evolutionary anatomy (ie number of limbs humans have)

development

progressive changes occurring during an organism's life where genotype is translated into phenotype

ecology

relationship b/w organisms and their physical environment

adaptation

evolutionary process by which natural selection fits organisms to their environment; is a consequence of selection

fitness

organism's ability to survive and reproduce to pass its genetic material to its offspring

trade-off

increase in performance/fitness of one trait causes decrease in performance of another; leads to increased morphological complexity; inevitable consequence of living in complex world

genetic disease

disease caused b/c of mutation in DNA sequence that is inherited genetically

sickle cell anemia

inherited disorder affecting shape of red blood cells; example of balancing selection b/c mutation causing this disease also confers resistance to malaria, so allele is sometimes selected FOR

chromosome

gene-carrying structure found in the nucleus. inherit our genes on these and get 23 total from each parent; each has specific characteristics associated w/ it (like eye color)

allele

different forms of a gene, "flavors" of a trait. two identical alleles = homozygous, two diff alleles = heterozgous - can be dominant or recessive

recessive vs dominant allele

allele is dominant if phenotype it codes for is expressed in heterozygous condition; recessive is opposite

balancing selection

occurs when natural selection maintains stable frequencies of two or more phenotypic forms in a population (ex: sickle cell anemia and malaria resistance where allele is both good and bad, depending on environment)

evolutionary hitchhiking

can be hard to work out which traits where targets of selection b/c traits are often correlated w/ each other; thus non-selected traits can "hitchhike" along w/ the selected traits (ex: dog body and snout size)

stabilizing selection

selection against the extremes ie selection for the average, keeps distribution in place and is the dominant mode of selection on phenotype

directional selection

moving the phenotype in one direction toward an extreme; individuals at one end of distribution curve have higher fitness than individuals in the middle or at the other end of curve

disruptive selection

selects against the average and favors individuals at both extremes of the phenotypic range (ex: mammal size)

sexual selection

selection directly related to access to mates and whether individual organism leaves offspring in the next generation (effects offspring, not the individual)

genetic drift

change in allele frequencies in a population due to chance; effects are most pronounced in small populations; example of evolution without natural selection/differential reproductive success

bottleneck effect

change in allele frequency following dramatic reduction in the size of a population ie natural disaster; example of evolution w/o natural selection but can be caused by selection inadvertently if population reduction is caused by disease

founder effect

change in allele frequencies as a result of the migration of a small subset of a population to establish a new colony; evolution/descent with modification but not selection based

adaptive change

driven by selection since depends on fitness of individuals in population, pertains to evolutionary changes that make organism more suited to its environment (natural selection)

non-adaptive change

evolutionary changes that are driven by chance ie mutation or genetic drift

mutation

random changes in the genome of an organism; can be expressed (affects phenotype) or not and can lead to either increase or decrease in fitness. is the ultimate source of variation in a population. most occur b/c of uncorrected errors in DNA replication but can also be due to environmental factors

mutation rate

frequency of new mutations per generation in an organism or population. human mutation rate not that fast but virus rate is rapid

migration

seasonal movement of organisms from one habitat to another in search of food, better conditions, or reproductive needs

gene flow

transfer of alleles from one population to another, resulting from the movement of fertile individuals or their gametes. can introduce new allele or increase/decrease frequency of existing alleles

hardy-weinberg principle/equilibrium

a non-evolving state of a population in which allele frequencies stay the same over time. population at hardy-weinberg equilibrium is not evolving, so none of the forces that can cause evolution are acting

hardy-weinberg equation

p^2 + 2pq + q^2 = 1 p = frequency of one allele and q = frequency of the other allele

allele frequency

how common an allele is in a population. one allele is represented by one letter (upper or lower case), frequencies are always a single letter and are represented by p or q in h-w

genotype frequency

how common a genotype is in a population. genotype represented by two letters (homozygous of upper or lower case and heterozygous). products of multiplication in h-w (p^2, 2pq, q^2)

parthenogenesis

asexual reproduction w/o males where an ovum/egg develops w/o fertilization/sper. 80+ species like lizards, amphibians, fish

bacteria

single-celled organisms that lack a nucleus, prokaryote, one of earliest organisms to evolve on Earth so laid the foundation for our evolution

archaea

one of the 3 great domains of life and one of the earliest organisms alongside bacteria, unicellular prokaryote, same genetic code as bacteria

eukaryotes

organisms with cells that have a nucleus, appeared in the fossil record 1.9 billion yrs ago, one of the 3 great domains in tree of life

prokaryote

unicellular organism that lacks a distinct nucleus and other specialized organelles, includes bacteria, cyanobacteria, and archaea

biological species concept

says that a species consists of populations of organisms that can reproduce/interbreed with one another and that are reproductively isolated from other populations

ring species

populations that can interbreed with neighboring populations but not with populations separated by larger geographical distances. can interbreed one way around the "ring" but not the other (example of california salamander subspecies)

cryptic species

one of two or more morphologically indistinguishable populations that cannot interbreed (indistinguishable to our eyes but not within DNA data)

morphological species concept

says that species are groups of individuals that are morphologically similar to one another but are morphologically distinct from other such groups. typically used instead of biological concept bc easier to distinguish visible diffs

chronospecies

two non-overlapping species, but with a richer fossil record we find those separate species are part of a continuum of change so we lump together under this term

type specimen

specimen selected to serve as a model/name bearer for that species. is permanently stored in a museum or other institution

synonymy

documents species name changes

speciation

evolutionary process in which one species splits into two or more species; emergence of new species/lineage that occurs if you disrupt reproduction

phyletic change

transformation/changes within lineages

anagenesis

change within a lineage/chronospecies

cladogenesis

splitting of lineage into more than one

allopatric speciation

most common geographic mode of speciation: populations become separated via dispersal or vicariance. under this, reproductive isolation can arise as byproduct of genetic changes that happen within the isolated populations

parapatric speciation

geographic mode of speciation where populations are adjacent and a new species/niche forms geographically adjacent to parent species, continuity of organisms on the landscape. under this, reproductive isolation can arise only if selection is strong and/or gene flow is weak. example of monkeyflowers in copper rich soils

sympatric speciation

uncommon geographic mode of speciation where new species forms within geographic area of its ancestor. uncommon b/c adjacency allows for exchange of genes. example of fruit fly with apple and hawthorn "races"

dispersal

population disperses to a new place; is a founder event so founder effect likely to take place. can lead to rapid evolution b/c of founder effect, fast genetic drift, and intense directional selection in new environment

vicariance

population is physically split by change in environment. example of formation of geographic features that separates population or climate change

polyploidy

condition in which an organism has extra sets of chromosomes, often b/c of failed cell division and is more common in plants. can lead to new species

zygote

fertilized egg

prezygotic barrier

reproductive barrier that impedes mating between species or hinders fertilization. might be habitat, temporal, behavioral, mechanical, or genetic isolation

postzygotic barrier

reproductive barrier where offspring develop but aren't reproductively viable. typical of hybrids like mules which have an odd number of chromosomes

habitat isolation

populations live in different habitats and do not meet and thus cannot reproduce. example of hawthorn vs apple fruit flies that mate/feed on diff plants

temporal isolation

form of reproductive isolation in which two populations mate/breed at different times. ex: fall field vs spring field cricket

behavioral isolation

reproductive isolation in which two populations have differences in courtship rituals or other types of behavior that prevent them from interbreeding. ex: eastern and western meadowlarks can't recognize each other's songs

mechanical isolation

morphological differences between species prevent fertilization

genetic isolation

might be genetic differences between species or egg may reject sperm based on sperm's genotype

sterility

the inability to reproduce, typically due to genetic factors

hybrid zone

region where two incipient species are only partially reproductively isolated and come in contact, producing at least some offspring of mixed ancestry

reinforcement

strengthening of mating isolation in response to selection against unfit hybrids. often sharpens the boundaries between species/increases the separation

taxa/taxon

group or level of organization into which one or more populations of organisms are classified

cladogram

diagram that depicts the relative degree of relatedness among taxa; branch length has no meaning here

sister group

the lineage/group most closely related to the species in question; on cladogram, these are two branches that share a node (common ancestor)

node

branch point on a cladogram, represent most recent common ancestor

apomorphy

derived evolutionary trait; specialized character unique to group/species (eg feathers)

synapomorphy

shared evolutionary innovation, such as feathers shared by birds. basis of cladograms (eg fur is a synapomorphy of cat and dog)

plesiomorphy

ancestral/primitive character state (eg scales, from which feathers evolved)

symplesiomorphy

shared primitive/ancestral character trait (backbone is a symplesiomorphy for cat and dog)

autapomorphy

evolutionary innovation/derived character that exists in just one taxon/one branch on a cladogram; unique feature that doesn't help us determine evolutionary relationships

homoplasy

a character state that evolved more that once on a cladogram, or evolves and is lost

outgroup

helps to determine what the primitive character versus the derived character state is. outgroup will only have the primitive character

character matrix

table of taxa (left/rows) and character states (top/columns) where each cell in the matrix is coded with the character state applicable for each taxon-character combination (typically 0 or 1). helps us understand organism relatedness and thus form cladograms

principle of parsimony

tells us to choose the simplest scientific explanation that fits the evidence (ie simplest answer is likely to be the correct one). with relation to tree-building: best hypothesis is the one requiring fewest evolutionary changes

cetacean

a member of the infraorder of marine mammals that includes whales, dolphins, and porpoises

long branch attraction

tendency of some phylogenetic inference methods to incorrectly infer too close a relationship among rapidly evolving taxa.

statistical inconsistency

property of increasing data where it increases support for the wrong answer

maximum likelihood

analysis that uses all sequence data to down-weight proposed synapomorphies by the probability that they might have arisen by chance given how different the sequences are overall; the more different, the more likely shared similarities are due to chance

phylogram

A phylogenetic tree in which branch lengths are proportional to strength of support and the number of genetic changes on the branch. lengths on these can be used to estimate divergence times

phylogeny

representation of evolutionary history and relationships between groups of organisms. branch lengths are proportional to time in these

taxonomies

system of classification

monophyletic group

contains an ancestral species and all of its descendant; also called a clade. ex: mammals or birds

paraphyletic group

contains an ancestral species and some, but not all, of its descendants. ex: reptiles b/c they exclude birds

polyphyletic group

rare grouping that contains distantly related species but not their most recent common ancestor. ex: vultures w/ their 3 feeding types or marine mammals

homology

similarity in structure, physiology, or development of deff species of organisms resulting from common ancestry. can treat as equivalent to synapomorphies

convergence/parallelism

unrelated organisms evolve structures, traits, or morphological features that have the same function. typically equivalent to homoplasies

phylogenetic species concept

claims that species are monophyletic groups, defining them as the smallest group of individuals on a phylogenetic tree. tends to overcount # of species compared to biological species concept

molecular clock

hypothesis that differences in DNA between species accumulate at a universal constant rate and thus DNA differences between living species could be used to date their times of divergence

neutral evolution

b

mutation vs substitution

mutations = changes in the DNA/creation of new allele; substitutions = fixation of a mutation/new allele fixed in population either by selection or drift and with or without additional mutational change.

synonymous mutation

mutation that is essentially neutral within genic regions of DNA, doesn't change the amino acid

nonsynonymous mutation

mutation in a gene that changes the amino acid sequence