Evolution Exam 1

-Why can viruses (Ex. flu) be difficult to fight? -How do new species arise in novel environments? -How did cetaceans transition from terrestrial to aquatic environments?

Pose three questions that biological evolution can potentially address (these 3 are from HW)

Georges Buffon

This early naturalist believed species could develop variations in traits in new environments; "earth is very old, and life has gradually changed during its history"

Carolus Linnaeus; kingdom, phylum, class, order, family, genus, species

This naturalist developed a classification system to organize organisms into taxa. "father of taxonomy"; what are the hierarchy levels of this system?

Georges Cuvier

This naturalist discovered that there were species that no longer existed after discovering mammoth and mastodon fossils in Europe and Siberia. "many fossils are the remains of extinct species"; his contributions founded the study of prehistoric life, known as paleontology

Tiktaalik

"missing link" thought to be a transitional fossil between fish and tetrapods. -Lived ~375 mya. -Displays a neck, wrist bones, but no digits.

Acanthostega

A member that belongs to the extinct taxa in the phylogeny of tetrapods to add more understanding of its evolution from aquatic vertebrates. -Lived ~365 mya. -Displays lungs and recognizable limbs, including digits, but NO wrists

Eusthenopteron

A member that belongs to the extinct taxa in the phylogeny of tetrapods to add more understanding of its evolution from aquatic vertebrates. -Lived ~385mya. -Displays tetrapod-like bone structure and internal nostrils

Pakicetus

A terrestrial ancestor of whales thought to have lived 10 million years ago. Serves as a link between whales and other common living terrestrial animals because it had a whale-like inner ear bone and an ankle bone displayed in a large order of even-toed, hoofed mammals such as hippos, pigs, cows, etc. Known as the "whale of Pakistan"

Archaeopteryx

An intermediate fossil that lived 145 mya, and shows both reptile and bird characteristics.

uniformitarianism; Darwin applied this theory to a geological formation (the Weldon Dome) and decided it alone probably took 300 years to form and that earth in its entirety was likely billions of years old.

Earth's landscapes have been shaped by the cumulative action of gradual, natural processes that are observable today. "the present is the key to the past"; how did this concept influence Darwin's thinking about evolution?

synapsids

tetrapods that emerged 300 million years ago and became the dominant terrestrial vertebrates about 20 million years later

diapsids (dinosaurs)

tetrapods that replaced synapsids as the dominant terrestrial vertebrate after they emerged in the fossil record around 240 million years ago. They display two temporal openings in the skull instead of one. They ruled the ecosystem until a mass extinction 65 mya

locus

the basic unit of inheritance; a specific location of a gene or a piece of DNA sequence on a chromosome

genetic recombination

the exchange of DNA segments of DNA between homologous chromosomes early in meiosis. This may lead to the production of new combinations of alleles, not present on a single parental chromosome

convergent evolution

the independent evolution of similar traits in unrelated species

point mutations; In a human germ line, there is a 1.2e-8 chance per base that a point mutation will occur. The genome size contains 3,200,000,000 bases. Therefore the number of mutations per generation that are likely to occur within the human genome is 38.4 (1.2e-8 x 3200Mb)

the largest frequency of mutations. Includes adding or deleting a single base from the DNA sequence. How big is the human genome and how likely are these types of mutations to affect the genome?

exaptation

the process in which existing structures take on new functions through descent with modification

evolutionary reversal

the reversion of a derived character state to its ancestral state

Horizontal gene transfer

the transfer of genetic material from one organism to another

Thomas Malthus

this 18th century economist contributed the idea that population growth in humans can be limited by the supply of resources

William Smith

this geologist organized rock strata into a geological history by using fossils. "different rock layers contain distinct fossils"

James Hutton

this geologist proposed that Earth was shaped through imperceptibly slow and perpetual changes, such as erosion and sedimentation.

Mary Anning

unearthed several species of extinct marine reptile fossils in South England.

tetrapod

vertebrates with four limbs, or descended from vertebrates with four limbs. Ex/ Silvanerpeton

synapsid jaw bones

what are mammalian inner ear bones homologous to?

Hippos; whales share many similarities with several mammals but hippos where determined to be the closest living terrestrial relative after comparing whale dna to other land mammals using genetic sequencing

what are the closest living terrestrial relatives of whales? How was this demonstrated?

sexual reproduction, recombination, and mutation

what are the major sources of heritable genetic variation?

Bacteria, Archaea, Eukarya

what are the three major branches for life?

autosomes (do not differ between sexes) & sex chromosome (differ between males and females)

what are the two types of chromosomes and how do they differ?

synapmorphy

what is a specific type of homology?

heritable variation

what is the "raw material of evolution?"

chordates; aquatic vertebrate

what lineage do humans belong to? What were the first of these to appear? *fossil record appeared 515 mya

Silvanerpeton (ab 370 mya)

what was the first terrestrial vertebrate and about what time did it appear?

150 million years ago

when did the first mammals appear?

the traits: -exhibited dominant and recessive inheritance patterns -were controlled by alternative alleles at one gene -had simple and discrete phenotypes with no in-between states

why were the pea traits that Mendel studies not reflective of most genetic traits?

-skin resistance to desiccation -structural support -new reproductive strategies -new respiration strategies

What adaptations were required before vertebrates could live on land?

1. organisms have descended with modification, from common ancestors 2. the chief cause of modification is natural selection acting on hereditary variation

What are the two major evolutionary hypotheses that Darwin proposed in The Origin of Species?

data from *isotopic analysis of fossil teeth* shows that the oldest relatives of cetaceans have isotope ratios consistent with animals that drink primarily freshwater (Higher levels of O16). As their lineage evolved, the most recent extinct cetacean ancestors have isotope ratios consistent with animals that drink primarily saltwater (higher levels of O18). One unique intermediate species, Ambulocetids, display large levels of both Oxygen isotopes, which suggests that they may have lived in both fresh and salt water environments. Because terrestrial animals drink freshwater and marine mammals drink salt water, this data serves as more evidence that whales likely evolved from land mammals.

What data is consistent with whales first evolving in freshwater? How does this appear across the cetacean lineage?

No relationship (an organism may have 12 chromosomes and more than 28,000 genes, as seen in the Norway spruce. Or it may have 23 chromosomes, nearly twice as many, and only have 20,000 genes.)

What is the relationship between genome size and gene number?

early cyanobacteria started producing oxygen as a waste product of photosynthesis, causing . a mass extinction of bacterial species that found oxygen to be toxic

What occurred during the "Great Oxygenation Event" (2.7-2.4 bya)?

"traits evolve within populations by the influence of environmental factors"

What scientific contribution did Charles Darwin and Alfred Wallace make that led scientists from natural theology to modern evolution?

Charles Lyell

a 19th century scientist that expanded on the ides of James Hutton. In doing so, he is responsible for the acceptance of uniformitarianism by the general scientific community

Cambrian explosion

a 20 million year period during which nearly all living animal lineages first appeared in the fossil record

scientific theory

a comprehensive, coherent body of interconnected statements, based on reasoning and evidence, that explain some aspect of nature

Ediacaran Fauna

a group of animals that existed between 570-540 mya and includes diverse species that bear little resemblance to animals alive today

fact

a hypothesis that has acquired so much supporting evidence that we act as if it is true

natural selection

a mechanism that can lead to evolution, whereby differential survival and reproduction of individuals cause some genetic types to replace other (i.e. survival of the fittest)

Radiometric dating; 4.6 billion years old

a method of dating geological or archeological specimens by determining the relative proportions of particular radioactive isotopes present in a sample; using this method how old were scientists able to determine the earth was?

frameshift; silent mutation (no change to protein sequence), missense mutation (change in one of the amino acids in the protein sequence), nonsense mutation (creates a premature stop codon and terminates translation early)

a mutation that shifts the "reading" frame of the genetic code by inserting or deleting a nucleotide base. What are the consequences of this type of mutations?

homology

a trait that is similar among species due to common ancestry

phylogeny

a visual representation of the evolutionary history of a species

nonsynonymous mutation

altered codon specifies for a different amino acid

synonymous mutation

altered codon specifies for the same amino acid

Durodon

an aquatic mammal with many characteristics of modern whales that is thought to have lived 4 million years ago. It displays mammalian like teeth, giving it its nickname "spear-tooth," plus vestigial hind limbs.

Burgess Shale

an exceptionally rich site for Cambrian fossils

hypothesis

an informed conjecture or statement of what might be true

Ambulocetus

ancestor to whales, suspected to have lived 20 mya, "walking whale"

biological evolution

any change in the inherited traits of a population that occurs from one generation to the next

nodes

branch points in a phylogeny that represents where lineages split (i. e. speciation events)

clades

branches of a phylogeny that contain a node and all of its descendants

synapmorphy

characteristic present in a common ancestor that is shared by its immediate evolutionary descendants

homoplasy; arise from either convergent evolution or evolutionary reversals

describes character state similarity NOT due to shared ancestry. How does this arise?

independent assortment

describes the RANDOM process by which each copy of a chromosome pair will end up in each cell

genotype

describes the genetic makeup of an individual (i.e. describes an individual's alleles)

segregation

describes what occurs in the final stages of meiosis, where in each pair of chromosomes separates, so that only a single copy ends up in each gamete

alleles

different variants in DNA sequence at the same locus

Nicolaus Steno

discovered fossilized shark teeth at the tops of mountains. After studying these fossils and the rock layers that contained them, he contributed the study of layering in rocks, known as stratigraphy

divergent evolution

evolution of one or more closely related species that have adapted to different ecological conditions and therefore no longer resemble each other (ex/ whales & hippos)

polytomy

evolutionary relationship (order of branching is uncertain)

Proximate causation

explanation of evolution that focuses on a mechanistic understanding of how something happened. Ex/ wing color in peppered moths is genetic. A specific gene codes for whether they have light or dark-colored wings. In moths that survive and reproduce, the genes for a specific color is passed to their offspring.

Ultimate causation

explanation of evolution that focuses on historical perspectives of how something came to be. Ex/ wings of peppered moths help the moths blend in. By blending in, their chances of survival increase. So in a specific environment, one wing color may help more moths survive than the other wing color, and therefore it appears this trait is passed more to offspring.

polyphyletic

group of organisms that does not share an immediate common ancestor, and is therefore not a legitimate clade

monophyletic clade

group of organisms that share a common ancestor and all of the descendants of that common ancestor

paraphyletic

group of organisms that share a common ancestor, but does NOT include all of the descendants of that common ancestor, and is therefore not a legitimate clade

somatic mutation

mutations that affect cells in the body of an organism. This type of mutation is NOT heritable, but it does often result in cancer.

Germ-line mutations

mutations that affect gametes. This type of mutation IS heritable

internal node

phylogenetic representation of ancestral species

branches

phylogenetic representation of lineage evolving through time (i.e. the newly formed species or subspecies

tip (terminal node)

phylogenetic representation of the lineages (species, populations, or genes) being compared

root (root node)

phylogenetic representation of the most recent common ancestor of all species in the tree

Ploidy; haploid (n), diploid (2n), triploid (3n), tetraploid (4n), etc.

refers to the number of copies of unique chromosomes in a cell. What are the different types?

Hypothetico-deductive method; hypothesis is either: rejected, modified, or accepted.

scientific inquiry proceeds by formulating a hypothesis that can be falsifiable, using a test on observable data where the outcome is not yet known. what are the potential outcomes to this method?

Lagerstatten

sites with an abundant supply of unusually well-preserved fossils from the same period of time

high levels of environmental oxygen, slow burial, scavengers present, not an aquatic environment, bacteria present, sun, wind, and rain

Common factors that inhibit fossilization are:

Observed: high birth rates should lead to exponential population growth, but population sizes are normally stable, and natural resources are limited. Inferred: more individuals are born than can survive, so there must be a fierce struggle for existence. Observed: No 2 individuals are exactly the same and this variation is typically heritable. Inferred: Those who survive this fierce struggle for existence is not random, but rather it is dependent on heritable variation, and if that variation increases survival, its frequency within populations will also increase.

Describe Darwin's observations and how they lead to the inferences he developed regarding natural selection and the evolutionary mechanism of change.

DNA is a linear molecule made up of two strands of nucleotides that wind together to form a double helix. Each nucleotide is made of a phosphate group, a 5-carbon deoxyribose sugar, and a base (Adenine, Guanine, Cytosine, or Thymine). DNA is further organized into chromosomes. There are 23 chromosome pairs (total of 46) in humans (22 somatic and 1 germ). Mitochondrial DNA, much like the DNA of most Bacteria and Archaea, is circular.

Describe the organization of DNA in a human cell & how it caries within and between species

Proteins are made from a combination of *20 different amino acids* that can be strung together in any order to make protein chains with different sequences and lengths. These protein chains fold into a variety of shapes such as sheets, cylinders, and other forms because the building blocks of proteins *vary in their affinities for water.* The final shape a protein takes on as it folds allows each protein to *do a precise task.*

Describe the structure of proteins

Lamarck believed that simple organisms always evolve into more complex organisms, and that traits acquired during a lifetime could be passed to offspring. In contrast, Darwin, believed that species share traits because they evolved from a common ancestor, and that some inherited traits get passed to offspring more frequently than others (but not all).

Discuss the differences in Darwin's and Lamarck's explanation of evolution

Jean-Baptiste Lamarck

Evolutionary scientist that observed anatomical similarities between species, and from these observations hypothesized that organisms acquire adaptations during their lifetimes and pass the adaptations to their offspring. "evolution occurs and is based on the inheritance of acquired traits." However, he was incorrect in thinking that phenotypic changes in individuals as a response to environmental conditions would make a permanent change in a trait that would be persist through subsequent generations.

-the bones that support the wings of birds, pterosaurs, and bats are arranged in the same order in each animal -the Pax6 gene in vertebrates and the eyeless gene in flies have similar sequences, and both regulate embryonic eye development -the pharyngeal arches found in all vertebrate embryos develop into gill supports in fish and throat structures in mammals

Give 3 examples of homologies and explain why they are

Fossils reveal that even some dinosaurs (velociraptors) had feathers, but they could not fly. They likely used their feathers for insulation and to warm their eggs. Many birds today use their feathers for flight, which displays an exaptation because this is not ancestral function of feathers. Other birds, such as penguins, do not have the ability to fly but they still have feathers that function much like those of the dinosaurs, displaying reverse evolution.

How are feathers a good example of exaptations and reverse evolution.

For a comparison examining the evolution of the mammalian ear bones, an outgroup that is a closely related species to mammals, but that does not have the same arrangement of ear bones would need to be used, i.e. birds and reptiles. Other mammals, wether extinct or living, cannot be used since they belong to the clade being studied.

How can phylogenies be used to trace the evolution of middle ear bones in mammals?

Earliest evidence of life is very controversial. Some believe they have found biomarkers in ancient *Zircons* that formed *4.1 bya*. Others argue the oldest fossils of *microbes* that have been discovered are *3.8 byo*. The most widely accepted evidence of life is *stromatolites,* which are layered structures formed by the mineralization of bacteria, and these were found to be *3.45 byo.*

How far back can we find evidence for life? How far back can we go and still find definitive evidence of life? What is that evidence?

Life likely originated more than once, but we still think all life comes from a common ancestor. One reason for this is that all life uses only the L optical isomer of amino acids.

How many times has life evolved on Earth? Describe evidence that supports the inference that all currently forms of life on Earth share a common ancestor.

Kelvin believed the rate of heat lost showed that the Earth was less than 20 million years old. His theory, however, was incorrect because it was based on a flawed assumption about the structure of the Earth's interior. (he believed that the planet was a rigid sphere)

How old did Lord Kelvin say the Earth was and why? Was he correct, why or why not?

less than 10 billion years old

How old is our galaxy?

300,00 years old

How old is the oldest known homo sapien fossil?

~14 billion years old

How old is the universe?

-reassortment can produce viral strains that can jump between species (such as birds and humans) -viral strains produced through reassortment may develop significantly different surface proteins (which may make it function differently; ex/ a mutated capsule protein allows it to invade the hose cell undetected) -some mutations can help a new strain of virus escape detection by the host's immune system in ways existing viruses cannot.

Identify characteristics of viruses that make them difficult to control, and are therefor favored by natural selection?

Scientists believed that a transitional fossil likely existed between the ages of 380 myo and 350 myo, placing it somewhere between the ages of the 2 already identified extinct taxa. They also decided that it likely lived in coastal wetlands or river deltas because it probably had the ability to live on both water and land

Scientists knew there likely had to have been a transitional fossil between the two existing extinct taxa (Eusthenopteron-385 mya & Acanthostega-365mya), but how did they know where to look and what where the characteristics they were looking for?

lobe-finned fishes (Coelacanths); long bones in tetrapod arms & legs are homologous with bones in fins

The closest living ancestor to all tetrapods. This theory is supported by the evidence that this organism's fossil shows the development of the tetrapod shoulder girdle, arm & wrist bones, and digits over time. * what traits of tetrapods are homologous with what traits of this organism?

Whales share similarities with fish (which likely arose from convergent evolution) and with mammals (which are considered to be synapomorphies; ex/ lungs, placenta, live birth, mammary glands, middle ear bones, hair in developing embryos). Because of this Darwin proposed that cetaceans (whales) descended from mammals that lived on land and their lineage evolved into a "marine mammal" via natural selection. Since his hypothesis several fossils of intermediate species show that "land whales" could have very possible existed. (ex/ dorudon, pakicetus, & ambulocetus)

how do whales demonstrate how lineages change through time?

~4.6 bill years ago (same as earth)

how old is our solar system?

Snowball Earth Hypothesis

hypothesis that an abrupt change in climate about 715 million years ago lead to a very cold Earth covered in ice from pole to pole. Likely due to an intense period of volcanic activity

Drought hypothesis; many characteristics of tetrapods made them poorly suited for life on land (long tearable tails, moist skin, etc.)

hypothesis that tetrapod limbs evolved in species that faced periods of drought. How does the phylogeny of tetrapods DISPROVE this theory?

genome; the human genome is diploid (contains 2 homologous copies of each chromosome)

includes all the hereditary information of an organism; what can be said about this information in humans?

teleosts

lineage of bony fish that comprises most aquatic vertebrates including goldfish, salmon & tuna

point mutation, insertion, deletion, gene duplication, inversion, chromosome fusion/fission, genome duplication

list different types of mutations