Bio 221 - midterm 1

Biological evolution

any change in the inherited traits of a population that occurs from one generation to the next (that is, over a time period longer than the lifetime of an individual in the population)

fossil

preserved evidence of life from a past geological age, including impressions and mineralized remains of organisms embedded in rocks

Lineage

refers to a chain of ancestors and their descendants. A lineage may be the successive generations of organisms in a single population, the members of an entire species during an interval of geological time, or a group of related species descending from a common ancestor

Natural selection

a mechanism that can lead to evolution, whereby differential survival and reproduction of individuals cause some genetic types to replace (outcompete) others

homologous characteristics

is similar in two or more species because it is inherited from a common ancestor

Dorudon

a 40-million-year-old whale, has different types of teeth, some of which have complicated surfaces. They bear a strong resemblance to the teeth of some extinct land mammals

synapomorphy

a derived form of a trait that is shared by a group of related species (that is, one that evolved in the immediate common ancestor of the group and was inherited by all its descendants)

Pakicetus

First terrestrial cetacean ever discovered, Although Pakicetus may not look like a whale, synapomorphies reveal its relationship to more familiar cetaceans. Here, we show the right ectotympanic bones of Pakicetus and a living dolphin species. The ectotympanic bone surrounds the middle ear cavity. The inner wall of the ectotympanic, known as the involucrum, is thick and dense in cetaceans—and in fossils such as Pakicetus. But this trait is found in no other living or fossil mammals. Other synapomorphies include features of the teeth and skull indicated on the skull of Dorudon

Ambulocetus

“walking whale” - has an involucrum, as well as other traits that are found today only in whales, It was the first fossil whale to be discovered with legs.

Morphology

refers to the form and structure of organisms

Phylogeny

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

Genus

a taxonomic group that includes species

mutation

any change to the genomic sequence of an organism

Viral reassortment

occurs when genetic material from different strains is mixed into new combinations within a single cell

Genetic drift

volution arising from random changes in the genetic composition of a population from one generation to the next

phenotype

a measurable aspect of organisms, such as morphology (structure), physiology, and behavior. Genes interact with other genes and with the environment during the development of the phenotype

The Great Chain of Being

According to this view, plants were the lowest forms of life, having only the capacity to grow. Animals occupied a higher position on the chain because, in addition to growth, they also had the ability to move. Humans were situated even higher, thanks to their powers of reason, a divine plan established by God at creation

Linnaean Classification (taxonomy)

the science of describing, naming, and classifying species of living or fossil organisms

taxon

refers to groups of organisms that a taxonomist judges to be cohesive units, such as species or orders

Stratigraphy

the study of layering in rock (stratification)

Paleontology

the study of prehistoric life

Extinction

refers to the permanent loss of a species. It is marked by the death or failure to breed of the last individual

Uniformitarianism

the idea that the natural laws observable around us now are also responsible for events in the past. One part of this view, for example, is the idea that Earth has been shaped by the cumulative action of gradual processes like sediment deposition and erosion

theory

an overarching set of mechanisms or principles that explain major aspects of the natural world. Theories are supported by many different kinds of evidence and experimental results

hypothesis

a tentative explanation for an observation, phenomenon, or scientific problem that can be tested by further investigation or experimentation

Homology

refers to the similarity of characteristics resulting from shared ancestry

homologous characteristic

similar in two or more species because it is inherited from a common ancestor

Descent with modification

refers to the passing of traits from parents to offspring. Darwin recognized that, over time, this process could account for gradual change in species’ traits and homology

Natural selection

a mechanism that can lead to adaptive evolution, whereby differences in the phenotypes of individuals cause some of them to survive and reproduce more effectively than others

Artificial selection

he selective breeding of animals and plants to encourage the occurrence of desirable traits. Individuals with preferred characteristics are mated or cross-pollinated with other individuals having similar traits

adaptation

an inherited aspect of an individual that allows it to outcompete other members of the same population that lack the trait (or that have a different version of the trait). Adaptations are traits that have evolved through the mechanism of natural selection

Heredity

the transmission of characteristics from parent to offspring

Genetics

the study of heredity, or how characteristics of organisms are transmitted from one generation to the next

gene

a segment of DNA whose nucleotide sequence codes for proteins, codes for RNA, or regulates expression of other genes

DNA

deoxyribonucleic acid, is a long, double-stranded molecule containing genetic information for development, life, and reproduction

Radiometric dating

a technique that allows geologists to estimate the precise ages at which one geological formation ends and another begins

isochron

a line on a graph, connecting points at which an event occurs simultaneously. Isochron dating is a technique to measure the age of rocks by determining how ratios of isotopes change in them over time

Lagerstätte

a site with an abundant supply of unusually wellpreserved fossils—often including soft tissues—from the same period of time

Burgess Shale

a Lagerstätte in Canada in which there is a wealth of preserved fossils from the Cambrian period

biomarker

molecular evidence of life in the fossil record. Biomarkers can include fragments of DNA, molecules such as amino acids, or isotopic ratios

hominin

includes humans as well as all species more closely related to humans than to chimpanzees. Within this group, humans are the only surviving members

stromatolite

a layered structure formed by the mineralization of bacteria

Bacteria

ne of the two prokaryotic domains of life. Domain Bacteria includes organisms such as Escherichia coli and other familiar microbes

Archaea

one of the two prokaryotic domains of life. Archaea superficially resemble bacteria, but they are distinguished by a number of unique biochemical features

Eukarya

he third domain of life, characterized by traits that include membraneenclosed cell nuclei and mitochondria. Domain Eukarya includes animals, plants, fungi, and protists (a general term for single-celled eukaryotes)

Ediacaran fauna

a group of animal species that existed during the Ediacaran period, just before the Cambrian. The oldest Ediacaran fossils are about 570 million years old. Ediacarans included diverse species that looked like fronds, geometrical disks, and blobs covered with tire tracks. They appear to have become extinct 540 million years ago, although some researchers argue that certain Ediacaran taxa belong to extant animal clades

chordate

a member of a diverse phylum of animals that includes the vertebrates, lancelets, and tunicates. As embryos, chordates all have a notochord (a hollow nerve cord), pharyngeal gill slits, and a post-anal tail. Many present-day chordates lose or modify these structures as they develop into adults

notochord

flexible, rod-shaped structure found in the embryos of all chordates. Notochords served as the first “backbones” in early chordates, and in extant vertebrates the embryonic notochord becomes part of the vertebral column

trilobite

was a marine arthropod that diversified during the Cambrian period. Trilobites gradually died out during the Devonian period

prokaryote

a microorganism lacking a cell nucleus or any other membrane-bound organelles. Prokaryotes comprise two evolutionarily distinct groups, the Bacteria and the Archaea

tetrapod

a vertebrate with four limbs (or, like snakes, descended from vertebrates with four limbs). Living tetrapods include mammals, birds, reptiles, and amphibians

teleost

a lineage of bony fishes that comprises most living species of aquatic vertebrates. They can be distinguished from other fishes by unique traits, such as the mobility of an upper jawbone called the premaxilla

synapsid

a lineage of tetrapods that emerged 300 million years ago and gave rise to mammals. Synapsids can be distinguished from other tetrapods by the presence of a pair of openings in the skull behind the eyes, known as the temporal fenestrae

branch

a lineage evolving through time that connects successive speciation or other branching events

Phylogeny

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

node

a point in a phylogeny where a lineage splits (a speciation event or other branching event, such as the formation of subspecies)

tip

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

internal node

a node that occurs within a phylogeny and represents ancestral populations or species

clade

a single “branch” in the tree of life; each clade represents an organism and all of its descendants

Monophyletic

describes a group of organisms that form a clade

Polyphyletic

describes a taxonomic group that does not share an immediate common ancestor and therefore does not form a clade

Paraphyletic

escribes a group of organisms that share a common ancestor, although the group does not include all the descendants of that common ancestor

character

a heritable aspect of organisms that can be compared across taxa

Synapomorphy

a derived form of a trait that is shared by a group of related species (that is, one that evolved in the immediate common ancestor of the group and was inherited by all of its descendants)

outgroup

a group of organisms (for example, a species) that is outside of the monophyletic group being considered. In phylogenetic studies, outgroups can be used to infer the ancestral states of characters

Homoplasy

describes a character state similarity not due to shared descent (for example, produced by convergent evolution or evolutionary reversal)

Convergent evolution

The independent origin of similar traits in separate evolutionary lineages

Evolutionary reversal

describes the reversion of a derived character state to a form resembling its ancestral state

Parsimony

principle that guides the selection of the most compelling hypothesis among several choices. The hypothesis requiring the fewest assumptions or steps is usually (but not always) best. In cladistics, scientists search for the tree topology with the least number of character-state changes—the most parsimonious

Polytomy

escribes an internal node of a phylogeny with more than two branches (that is, the order in which the branchings occurred is not resolved)

Tiktaalik

had long limb bones, and it also had small bones homologous to those in our wrists, had a neck that allowed its head to move independently, has a number of unique features that are not seen in other lobe-fins and that tetrapods do not share

exaptation

a trait that initially carries out one function and is later co-opted for a new function. The original function may or may not be retained

protein

an essential macromolecule for all known forms of life. Proteins are threedimensional biological polymers constructed from a set of 20 different monomers called amino acids

amino acid

the structural unit that, among other functions, links together to form proteins

Deoxyribonucleic acid (DNA)

an essential macromolecule for all known forms of life (along with RNA and proteins). DNA is a double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell’s proteins

Ribonucleic acid (RNA)

an essential macromolecule for all known forms of life (along with DNA and proteins). RNA differs structurally from DNA in having the sugar ribose instead of deoxyribose and in having the base uracil (U) instead of thymine (T)

nucleotide

he structural unit that links together to form DNA (and RNA). Each nucleotide includes a sugar (like deoxyribose or ribose) and a base.

Base

Refers to one of four nitrogen-containing molecules in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). (In RNA, uracil (U) replaces T.)

Ploidy

Refers to the number of copies of unique chromosomes in a cell

sex chromosome

a chromosome that pairs during meiosis but differs in copy number between males and females. For organisms such as humans with XY sex determination, X and Y are the sex chromosomes. Females are the homogametic sex (XX) and males are the heterogametic sex (XY).

autosome

a chromosome that does not differ between sexes

gene

a segment of DNA whose nucleotide sequences code for proteins or RNA or regulate the expression of other genes

Gene expression

the process by which information from a gene is transformed into a product

RNA polymerase

he enzyme that builds the single-stranded RNA molecule from the DNA template during transcription

Transcription

the process that takes place when RNA polymerase reads a coding sequence of DNA and produces a complementary strand of RNA, called messenger RNA (mRNA)

Messenger RNA (mRNA)

consists of molecules of RNA that carry genetic information from DNA to the ribosome, where it can be translated into protein

Translation

the process that takes place when a strand of mRNA is decoded by a ribosome to produce a protein

Transfer RNA (tRNA)

a short piece of RNA that physically transfers a particular amino acid to the ribosome

Gene control region

an upstream section of DNA that includes the promoter region as well as other regulatory sequences that influence the transcription of DNA

repressor

a protein that binds to a sequence of DNA or RNA and inhibits the expression of one or more genes

transcription factor

a protein that regulates the expression of a gene by binding to a specific DNA sequence in association with the gene sequence. A single transcription factor can regulate many genes if they share the same regulatory sequence

enhancer

a short sequence of DNA within the gene control region where activator proteins bind to initiate gene expression

MicroRNA

escribes one group of RNAs that act as post-transcriptional regulators of gene expression. MicroRNAs bind to complementary sequences on specific mRNAs and can enhance or silence the translation of genes. The human genome encodes more than 1000 of these tiny RNAs

hormone

a molecular signal that flows from cells in one part of the body to cells in other parts of the body. Hormones act directly or indirectly to alter the expression of target genes

RNA splicing

the process of modifying RNA after transcription but before translation, during which introns are removed and exons are joined together into a contiguous strand

Alternative splicing

The process of combining different subsets of exons together, yielding different mRNA transcripts from a single gene

Epigenetic

refers to the functional modifications to DNA that don’t involve changes to the sequences of nucleotides. Epigenetics is the study of the heritability of these modifications

population

a group of interacting and potentially interbreeding individuals of a species

Population genetics

the study of the distribution of alleles within populations and the mechanisms that can cause allele frequencies to change over time

Genetic locus

Refers to the specific location of a gene or piece of DNA sequence on a chromosome. When mutations modify the sequence at a locus, they generate new alleles—variants of a particular gene or DNA region. Alleles are mutually exclusive alternative states for a genetic locus