BIOEE 1780 Prelim 1

evolution

a process by which populations of organisms change over time

science

the use of evidence to construct testable explanations and predictions of natural phenomena as well as the organization of knowledge generated through the process

viruses

smallest living things

lineage

a chain of ancestors and their descendants

natural selection

a mechanism that can lead to evolution; differential survival or reproduction of individuals causes some genetic types to replace (outcompete) others

convergent evolution

the independent origin of similar traits in separate lineages

homologous

characteristics are similar in two or more species because they are inherited from a common ancestor

synapomorphy

a derived form of a trait that is shared by a group of related species; evolved in immediate common ancestor of the group and was inherited by all the descendants;

phylogeny

a visual representation of the evolutionary history of populations, genes, or species

mutations

any change in sequence of an organism

viral reassortment

when genetic material from different strains gets mixed into new combinations within a single individual

phenotypes

measurable aspects of organisms such as morphology, physiology and behavior

Carl Linnaeus

father of modern taxonomy; organized all living things into a single hierarchy of groups called TAXA

taxa

group of organisms that a taxonomist judges to be a taxonomic unit

taxonomy

introduced by Carl Linnaeus; the science of describing, naming, and classifying species of living or fossil organisms

Nicolaus Steno

naturalist; realized remains of animals and plants were sometimes preserved and transformed into stone; argued that over time, a sea must have covered the mountains and when shelled animals died and fell to the ocean floor, they were covered in sediments and turned to rock; father of geography and stratigraphy (study of layering in rock)

Georges Buffon

proposed that the Earth was very old and that life had gradually changed during its history

paleontology

study of prehistoric life

Georges Cuvier

helped establish that many fossils were the remains of extinct species

extinction

permanent loss of a population or species, arising with the death or failure to breed of the last individual

James Hutton

realized rocks formed through imperceptibly slow changes; ordering of layers of rock formed and studying of fossils

William Smith

discovered that layers of rocks contain distinctive groups of fossils; helped to organize strata into geological history based on the location of the fossil

Jean-Babtiste Lamarck

developed early theory of evolution; argued that complex species had evolved from simple ones by a mechanism of heredity through which the acquired traits were passed down; species were not fixed

epigenetic changes

acquired through life and passed on

Charles Darwin

naturalist; spent five years aboard HMS Beagle gathering fossils of extinct mammals ; all living things share a common ancestry; rejected mechanisms such as Lamarck's ladder of progress (proposed simpler process based on variation and selection--descent with modification)

Charles Lyell

proposed that all of life on Earth formed by small changes over time--uniformitarianism; popularized Hutton's idea that the Earth was shaped by gradual processes

Alfred Russel Wallace

came up with a mechanism for evolution similar to Darwin's idea of natural selection; sent letter to Darwin asking ideas to be presented to the Linnaean Society

homology

the similarity of characteristics in different species because of a common ancestor

homologous traits

similar because they are inherited from a common ancestor

analogous traits

similar because they have converged on a shared form but not derived from a common ancestor

Thomas Malthus

english clergyman whom Wallace and Darwin both derived ideas from; proposed that those who could adapt to society's needs to produce useful work would be able to survive and reproduce

adaptations

inherited aspects of an individual that allow it to outcompete other members of a population that lack the trait; evolve through natural selection

sexual selection

when individuals of one sex compete with each other over access to individuals of the other sex which can lead to evolution of traits that improve an individuals chances of mating

genetic drift

also a mechanism of evolution; random change in the frequency of traits or genetic variants that arises across generations due to random events; most pronounced in small populations

tips

terminal ends of an evolutionary tree, representing species, molecules, or populations being compared

branches

lineages evolving through time between successive speciation events

node

a point in a phylogeny where a lineage splits (a speciation event)

internal nodes

nodes within a phylogeny representing ancestral populations or species

clade

an organism and all of its descendants

monophyletic

a term used to describe a group of organisms that form a clade

characters

heritable aspects of organisms that can be compared across taxa

Taxon (or taxa)

a group of organisms that a taxonomist judges to be a taxonomic unit, such as species or order

cladogram

a phylogeny constructed by grouping taxa into nested hierarchies using information from synapomorphies

cladistics

phylogenetic methods that construct trees by grouping taxa into nested hierarchies (clades) according to their shared derived characters (synapomorphies)

homoplasy

character state similarity NOT due to shared descent (e.g., produced by convergent evolution or evolutionary reversal); can create the mistaken impression that species are closely related when they are not

convergent evolution

the independent origin of similar traits in separate evolutionary lineages

evolutionary reversal

the reversion of a derived character state to its ancestral state

systematics

identifying synapomorphies to generate phylogenies

exaptations

a trait that originates performing one function and which is later co-opted for a new function (ex. feathers-evolved originally for other functions than flight i.e. insulation, courtship display, and nest brooding)

Australopithecines

members of the hominid genus Australopithecus; still had snouts and chimpanzee-sized brains but had more adaptations for walking upright and arboreal life; evidence that bipedalism evolved long before an increase in brain size

mammalian ear

made up of modified parts of the lower jaw

coalescence

the process by which, looking back through time, the genealogy of any pair of homologous alleles merges in a common ancestor

genealogies

possible to trace back through time, reconstructing when mutations generated new alleles and how these alleles subsequently spread

gene tree

the branched genealogical lineage of homologous alleles that traces their evolution back to an ancestral allele

maximum parsimony

a statistical method for reconstructing phylogenies which identifies the tree topology that minimizes the total amount of change, or the number of steps, required to fit the data to the tree

positive selection

accumulation of an unusually high level of substitutions that change the structure of proteins

purifying selection

also called negative selection; removes deleterious alleles form a population; common form of stabilizing selection

bootstrapping

a statistical method for estimating the strength of evidence that a particular node in a phylogeny exists

distance-matrix methods

methods that construct phylogenetic trees by clustering taxa based on the proximity (or distance) between their DNA or protein sequences; place closely related sequences under the same interior node, and they estimate branch lengths from the observed distances between sequences

neighbor-joining

a distance method for reconstructing phylogenies; identifies the tree topology with the shortest possible branch lengths given the data

Maximum likelihood methods

focus on finding the tree that is "most likely" given the data set and model; begin with an explicit model of evolution at the molecular level and used to evaluate how well data support a given tree; compare likelihood scores for many different possible trees, and find tree that best fits data and model for molecular evolution

Bayesian methods

focus on evaluating the probability of a given tree being correct; start with possible tree and then make small changes to its topology over and over again and then converge on a set of most likely trees

Restriction enzymes

enzymes produced mostly by bacteria that recognize specific nucleotide sequences within DNA; cleave the DNA, resulting in fragments of different lengths depending on the source of the enzyme

micro satellites

noncoding stretches of DNA containing strings of short, repeated segments; the number of repetitive segments can be highly polymorphic so these are valuable genetic characters for comparing populations and assigning relatedness among individuals

synonymous substitutions

mutations that do not alter the amino acid sequence of a protein; these mutations do not affect the protein an organism produces, so they are less prone to selection and often free from selection completely

non-synonomous substitutions

also called replacement substitutions; mutations that alter the amino acid sequence of a protein; these can affect the phenotype and are therefore more subject to selection

molecular clock

a method used to determine time based on base-pair substitutions; use the rates of molecular change to deduce the divergence time between two lineages in a phylogeny; work best when they can be calibrated with other markers of time, such as fossils with known ages

neutral theory of molecular evolution

describes the pattern of nucleotide sequence evolution under the forces of mutation and random genetic drift in the absence of selection; under these conditions, substitution rate should equal the mutation rate

domains

Archaea, Bacteria, and Eukarya

prokaryotes

domain with a lack of a nucleus and of membrane-closed organelles

peptidoglycan

contained in the cell walls of almost all bacteria; lacking in the cell walls of archaea and eukarya

Gram stain

laboratory technique used to classify most types of bacteria into two distinct groups, Gram-positive and Gram-negative; smear of bacterial cells on a microscope slide is soaked in a violet dye and treated with iodine then washed with alcohol and counterstained with red safranin

gram-positive bacteria

retain the purple dye; have a thick cell wall containing about five times as much peptidoglycan

gram-negative bacteria

retain the red safranin counter stain; have a periplasmic space between the cell membrane and the distinct outer membrane

spirilla

bacteria in the shape of spirals

bacilli

bacteria in the shape of rods

cocci

bacteria in the shape of a sphere

lateral gene transfer

the transfer of genes from one species to another, common among bacteria and archaea

high-GC gram positives

produce important antibiotics; also known as actinobacteria; have more G-C nucleotide base pairs; develop an elaborately branched system of filaments that resembles the filamentous growth habit of fungi

low-GC gram positives

also known as firmicutes; low ratio of G-C nucleotide base pairs; can produce heat-resistant structures called endospores

mycoplasmas

group of low-GC Gram-positives that lack cell walls and are among the smallest cellular organisms

cyanobacteria

blue-green bacteria; photosynthetic bacteria that utilize Co2 and water and release oxygen into the atmosphere; may be unicellular or multicellular; use chlorophyll a for photosynthesis and fix nitrogen; extensive internal membranes

spirochetes

have unique structures called axial filaments that allow them to move in a corkscrew-like manner (ex. syphilis, lyme disease)

proteobacteria

mitochondria of eukaryotes derived through endosymbiosis of this; largest number of known species of bacteria; very diverse: aerobes, anaerobes, heterotrophs, photoautotrophs, chemoautotrophs, nitrogen fixers, big, small

autotroph

fix their own carbon

heterotroph

ingest already fixed carbon

photoautotrophs

an organism that obtains energy from light and carbon from carbon dioxide

chemoheterotroph

an organism that must obtain both carbon and energy from organic substances; critically important as decomposers (degrading organic matter)

Rhizobia

live in root nodules; leguminous plants that create these clumps that are colonized by bacteria and fix nitrogen and put it into the soil as a usable form for the plant

Binary Fission

asexual reproduction all prokaryotes do; replicated chromosomes then split cell wall and divide continuously

Conjugation

genetic exchange between two individuals, separate from the process of reproduction (which occurs by binary fission)

Phage conversion (transduction)

genetic exchange mediated by a phage (virus); phage attacks bacterium and inserts DNA/RNA which then gets incorporated into the host genome

Transformation

damaged cell leaks DNA other cells transport it through the membrane and incorporate it into their DNA

chlamydias

very small, all are obligate parasites; most common STD in US

extremophiles

archaea able to live under extreme conditions

acidophile

able to live in extremely acidic environments

halophile

able to live in hypertonic and alkali environment (very basic)

methanogens

contribute to global warming; anaerobic; found in hydrothermal vents, paddy fields, and mammalian guts

mitochondria

derived from a proteobacterium; powerhouse of the cell; produces ATP

endosymbiosis

incomplete phagocytosis of prokaryotes results in membrane bound organelles of eukaryotes; acquisition of a complete organism