Bio Quiz 2

What is a synapomorphy?

A shared derived character similarity. E.g., with all forms of life (Bacteria, Archaea, & Eukarya) as our frame of reference, the similarity between any 2 eukaryotes (say you & a redwood tree) in having a nucleus. The nucleus is a new feature not found in Bacteria.

What are the 2 main hypotheses for the transition from a nonliving state of matter to a state that meets the definition of life ??

Hypothesis 1: membrane & self-replicating molecules came early in the process, & metabolism came late. • Hypothesis 2: metabolism came early in the process, & membrane & self-replicating molecules came late.

Which, if any, of the circled groups meets the definition... "A set of species... that includes the most recent common ancestor (MRCA) of the set.... and some but not all of the species descended from that MRCA" ?

1 group meets the definition of a paraphyletic group: Group b (red), with MRCA at 3

Which, if any, of the circled groups meets the definition... "A set of species... that does NOT include the most recent common ancestor (MRCA) of the set."

1 group meets the definition of a polyphyletic group: Group a (black), with MRCA at 3.

What are the properties of life as defined in Biology ? (8 items in this list from Bio 200. How many can you name ?)

1. Life is highly ordered/structured 2. Life requires energy & processes that energy to drive its processes 3. Living things grow and develop 4. Living things reproduce 5. Living things respond to environmental stimuli 6. Living things show regulation 7. Living things show evolutionary adaptation via natural selection 8. Living things consist of one or more cells

What were the properties of early Earth's environment (5 points in this list) ?

1. Reducing or neutral atmosphere. No free oxygen. 2. Intense ultraviolet radiation at surface. 3. Abundant volcanic eruptions .4. Atmosphere of N, NOx, methane, carbon dioxide, ammmonia, hydrogen 5. Oceans at 40 - 50 °C

What are the necessary conditions for natural or abiotic selection ? (4 items on this list)

1. reproduction: "things" make copies of themselves or get copied 2. variation: at least some of the "things" show some differences with the other "things" 3. heritability: the differences among the "things" are passed on when the "things" are copied 4. fitness differences: the differences among things affect their survival (stability, persistence) and/or copying rate

Which, if any, of the circled groups meets the definition... "A set of species... that includes the most recent common ancestor (MRCA) of the set.... and all of the species descended from that MRCA" ?

2 groups meet the definition of a monophyletic group: Group c (blue), with MRCA at 6 Group d (green), with MRCA at 3.

Suppose the most recent common ancestor of present-day species A, B, C & D has the ancestral state of a certain character (say only 1 middle-ear bone). Suppose also that somewhere along the lineage marked by the red line, this character evolved from the ancestral state (1 middle-ear bone) to a derived character state (3 middle-ear bones). Which present-day species, if any, should have 3 middle-ear bones ? Which present-day species, if any, should retain 1 middle-ear bone ?

3 middle-ear bones (derived state): present-day species B & C 1 middle-ear bone (ancestral state): present-day species A & B

What is the earliest date for clear fossil evidence of life on earth?

3,400,000,000 years (3.4 billion)

Suppose we were back in time just after speciation events 2 & 5 had occurred, but before any subsequent speciation events had occurred (i.e., speciation events 1, 4 & 6 had not yet occurred). How many species would we see ?

4 species: lineage ancestral to A & B, lineage ancestral to C, lineage ancestral to D & E, & lineage ancestral to F & G.

What age is used for the age (formation) of Earth ?

4,600,000,000 years (4.6 billion)

What is a clade ?

A clade is a complete branch of an evolutionary tree, a.k.a. a monophyletic group.

The part of the figure being pointed to by the upper red arrow represents _____.

A contemporary species

What is the definition of a paraphyletic taxon ?

A paraphyletic taxon, formally defined as... a set of species... that includes the most recent common ancestor of the set (MRCA), and some but not all of the species descended from the MRCA. Informal definition: an incomplete branch of an evolutoinary tree. Turn

What do we call a tree diagram with an explicit scale for the amount of evolutionary change along a branch ?

A phylogram.

What is the definition of a polyphyletic taxon ?

A polyphyletic taxon, formally defined as... a set of species... that does NOT include the most recent common ancestor of the set (MRCA) ! Informal defintion: parts of 2 or more different branches of an evolutonary tree. Turn

What is the definition of a symplesiomorphy ?

A shared ancestral similarity. E.g., with all living organisms (Bacteria, Archaea & Eukarya) as our frame of reference, the similarity between you and the bacterium Escherichia coli in having ATP as the energy currency powering metabolism and a bounding plasma membrane that is a phospholid bilayer.

The earliest vertebrates from over 500 million years ago had a tail, and most living vertebrates have retained this feature, at least in their embryos. Among amphibians, salamanders have a tail but frogs & toads have lost it in the adult stage. Among mammals, monkeys have a prominent tail but the great apes largely have lost it. In us, we know it as our "tail bone" or coccyx, The shared similarity between salamanders and monkeys in having a tail therefore is an example of _____.

A symplesiomorphy (shared ancestral similarity).

What is a "taxon" ?

A taxon is a named group of organisms in a classification system. It can be a group at any level of the classificaton system: e.g., the bacterial species Escherichia coli (a.k.a. E.coli) is a taxon; e.g., the domain Eukarya (all eukaryotes) is a taxon. The plural of taxon is taxa.

What evidence supports the hypothesis that all living things are descended from a single common ancestor ? (8 points in this list - can you name them all ?)

All living organisms share the following: 1. Phospholipid bilayer membranes 2. Use of proton gradients to drive metabolic processes 3. Mechanism of DNA expression 4. 5' to 3' DNA synthesis 5. Ribosomes with ribozyme at core 6. Use of ATP as energy currency, & mechanism of synthesis of ATP 7. "Universal" genetic code 8. Use of DNA for storing information

What sorts of organic molecules of interest to us can be produced by "abiotic synthesis" ?

Amino acids, nitrogenous bases, lipids, & simple polymers of these like proteins & nucleic acids.

The part of the figure being pointed to by the lower red arrow represents _____.

An ancestral species.

What apparent problem with hypotheses about the origin of life did Nobel Laureate Jack Szostak study, & .... what did he discover ?

Apparent problem: Mg++ is necessary for RNA replication, but Mg++ degrades lipid bilayers. Szostak discovery: the common compound citrate prevents destruction of lipid biayers.

What can we say about the relative ages of the branching events marked with "b" and "c" ?

Branching event "b" occurred about 23 million years ago (mya) and branching event "c" occurred about 32 mya, so "b" is younger (occurred more recently) than "c". We can say this because this tree diagram has an explicit time scale & so is a chronogram.

Each of the 3 encircled groups represents an example of what kind of taxon ?

Each is an example of a monophyletic taxon, defined as... a set of species... that includes the most recent common ancestor of the set (MRCA), and all of the species descended from the MRCA. E.g., The green dot marks MRCA for the green group, which includes contemporary species A, B & C, all decendants of the green MRCA. There are no other species that are descended from the green MRCA that are not included in the green group. So the green group is monophyletic. You should be able to express the same sort of argument for the blue & red groups.

Each of the 3 encircled groups represents an example of what kind of taxon ?

Each is an example of a paraphyletic taxon, defined as... a set of species... that includes the most recent common ancestor of the set (MRCA), and some but not all of the species descended from the MRCA. E.g., The red dot marks MRCA for the red group (agreed ?), which includes contemporary species C, D, E, F & G, all decendants of the red MRCA. But contemporary species A & B also are descended from the same red MRCA but are not included in the red group. So the red group is paraphyletic. You should be able to express the same sort of argument for the blue & yellow groups.

Each of the 3 encircled groups represents an example of what kind of taxon ?

Each is an example of a polyphyletic taxon, defined as... a set of species... that does NOT include the most recent common ancestor of the set (MRCA) ! E.g., The green dot marks MRCA for the green group, which includes contemporary species B & G, both decendants of the green MRCA. But the green MRCA itself is NOT included in the green set. So the green group is polyphyletic (parts of 2, in this case, different branches). You should be able to express the same sort of argument for the blue & red groups.

What features are shared by the 2 hypotheses for the origin of life that we covered ? (3 in this list)

Features in common between the 2 hypotheses for the origin of life: 1. abiotic synthesis of organic molecules 2. a mechanism to reduce dilution of abiotically generated organic molecules 3. "abiotic selection" (~natural selection) favoring stability, persistence, self-replication, etc., of pre-biotic molecules.

What can we say about the relative ages of the branching events marked with "1" and "5" ?

In a basic tree diagram (cladogram) like this, we can't say anything about their relative ages. "1" could have occured more recently than "5", or longer ago, or at about the same time in the past !

What do we call a tree diagram like this with an explicit time scale?

It is called a chronogram.

Legless lizards and snakes both are....well, legless. With 4-limbed vertebrates (tetrapods) as our frame of reference, what kind of similarity is this between legless lizards and snakes ?

It is homoplasy, an independently evolved similarity. "Leglessness" (loss of legs) evolved in the lineage leading to snakes, and again in a lineage of "legged" lizards leading to legless lizards. BTW, legless lizards don't get confused with snakes or not for very long. Legless lizards have lots of lizard characteristics, like an external ear opening & moveable eyelids that snakes don't have. Turn

What is meant by the "abiotic synthesis of organic compounds"?

It means that non-living physical & chemical processes can result in the formation of organic compounds. E.g., lightning or UV radiation striking through the early earth's atmosphere.

Time Model for BH 201 & BH 202. Ignore if not your room. Which label corresponds to the Great Oxygenation Event, and what date is that ?

Label D, at about 2,400,000,000 (2.4 billion) years ago

Time Model for BH 423. Ignore if not your room. Which label corresponds to the Great Oxygenation Event, and what date is that ?

Label D, at about 2,400,000,000 (2.4 billion) years ago

Time Model for BH 201 & BH 202. Ignore if not your room. Which label corresponds to the earliest widely accepted fossil evidence of life on Earth, and what date is that ?

Label E, at about 3,400,000,000 (3.4 billion) years ago.

Time Model for BH 423. Ignore if not your room. Which label corresponds to the earliest widely accepted fossil evidence of life on Earth, and what date is that ?

Label E, at about 3,400,000,000 (3.4 billion) years ago.

What are the groups that are descendants of the lineage enclosed in the red oval ?

Lizards, dinosaurs & birds.

We covered 2 hypotheses that suggest different mechanisms for the transition from an abiotic state of matter to a state that meets our definition of life. How do these 2 hypotheses differ on where (in what kind of environment) the transition from non-living to living states of matter occurred ?

Membranes-early hypothesis: "warm little ponds," like splash ponds on the oceanic shores of continents. Membranes-late hypothesis: at deep-sea vents

We covered 2 hypotheses that suggest different mechanisms for the transition from an abiotic state of matter to a state that meets our definition of life. How do these hypothesses differ on the mechanism thought to function to resist dilution by diffusion of the molecular products of abiotic synthesis ?

Membranes-early hypothesis: a lipid membrane of some sort. Membranes-late hypothesis: the porous mineral crust coating deep-sea vents.

We covered 2 hypotheses that suggest different mechanisms for the transition from an abiotic state of matter to a state that meets our definition of life. How do these 2 hypotheses differ on when in the process metabolism appeared ?

Membranes-early hypothesis: gradually but later in the process. Membranes-late hypothesis: gradually but from the very beginning of the process

We covered 2 hypotheses that suggest different mechanisms for the transition from an abiotic state of matter to a state that meets our definition of life. How do these 2 hypotheses differ on what was the earliest "thing" that could self-replicate ?

Membranes-early hypothesis: simple RNA molecule. Membranes-late hypothesis: cyclical chemical reaction.

We covered 2 hypotheses that suggest different mechanisms for the transition from an abiotic state of matter to a state that meets our definition of life. How do these 2 hypotheses differ on when in the process plasma membranes appeared ?

Membranes-early hypothesis: well.......they appeared very early in the process. :) Membranes-late hypothesis: yup, you guessed it - they appeared at the very end of the process.

What is the definition of a monophyletic group?

Monophyletic taxon, formally defined as... a set of species... that includes the most recent common ancestor of the set (MRCA), and all of the species descended from the MRCA. Informal definition: a complete branch of an evolutionary tree.

The red arrow in this figure points to a "thread" that represents _____.

One population in a lineage.

What can we say about the relative ages of the branching events marked with "4" and "5" ?

Speciation event "4" is younger (occurred more recently) than speciation event "5."

To what living species is Species C most closely related ?

Species C is most closely related to species A & B, and equally closely related to both. Species C's MRCA with Species A is at "2" on the tree, and this also is Species C's MRCA with Species B.

Is Species G more closely related to Species D or to Species C ?

Species G is more closely related to Species D than it is to Species C. Species G's MRCA with Species D is at branching point 5, whereas Species G's MRCA with Species C is at branching point 3. Branching point 5 occurred more recently (closer to the present) than did branching point 3.

On this phylogram, the amount of evolutionary change along a branch is measured in what units ?

Substitutions per (nucleotide) site on a particular gene.

What are the 3 kinds of similarity among different organisms that we recognized ?

Synapomorphy - shared derived similarity Symplesiomorphy - shared ancestral similarity Homoplasy - independently evolved similarity

Time Model for BH 201 & BH 202. Ignore if not your room. On this model, what distance would correspond to the approximately 400 years of European history in the US ?

The 400 years of European history in the US would be represented by a line running back from the present time for a distance of about 3 ten-thousands of an inch (0.000267 in), about one tenth the smallest thing your (young) eyes can see.

Time Model for BH 423. Ignore if not your room. On this model, what distance would correspond to the approximately 400 years of European history in the US ?

The 400 years of European history in the US would be represented by a line running back from the present time for a distance rather less than 1 ten-thousands of an inch (0.000016 in), about one fifteenth the smallest thing your (young) eyes can see.

Suppose species C & E share a derived character state for a given character, but all the other contemporary species (A, B, D, F & G) retain the ancestral state of the same character. How might this pattern of character states have evolved ?

The derived character state might have evolved 2 times independently. For example, it might have evolved sometime since the branching point labeled "2" along the lineage leading to C, and it also might have evolved along the lineage from 4 to E. This process can be called convergent evolution, and the resulting independently evolved similarity is called homoplasy.

What can we say about the lineage marked by the red line ?

The lineage marked by red represents ancestors of present-day species B that are not ancestors of contemporary species A, C or D.

What can we say about the point on the tree marked by the red arrow ?

The red arrow points to the... most recent common ancestor of present-day species A, B, C & D.

Time Model for BH 423. Ignore if not your room. On this model, what distance would correspond to the approximately 10,000 years of human civilization ?

The roughly 10,000 years of human history would be represented by a line running back from now for a distance of about 4 thousands of an inch (0.004 in), about the thickness of of sheet of copy paper.

Time Model for BH 201 & BH 202. Ignore if not your room. On this model, what distance would correspond to the approximately 10,000 years of human civilization ?

The roughly 10,000 years of human history would be represented by a line running back from now for a distance of about 7 thousands of an inch (0.0067 in), about one & a half times the thickness of of sheet of copy paper.

All mammals share the similarity of having hair & mammary glands but these characters are not present in the other 4-limbed vertebrates (amphibians, reptiles & birds), including the reptiles from which mammals evolved. What do we call these 2 similarities between any 2 mammals, if the frame of reference is the 4-limbed vertebrates?

These similarities between any 2 mammals are synapomorphies (shared derived similarities).

Is Species A related to Species D ?

Yes, they are related. Their most recent common ancestor is at branching point 3.

This structure, which we called a _____, was used to represent a section of a branch of a tree diagram.

lineage