Bio 209 Chapter 9 test two

If there are roughly 65,000 DNA nucleotide base pair differences between humans and mice currently and it has been about 65 million years since they had a common ancestor, this translates to roughly what molecular clock rate? Make sure to include your units.

1 nucleotide base pair difference per 1000 years

If there are roughly 65,000 DNA nucleotide base pair differences between species A and B currently and it has been about 65 million years since they had a common ancestor, this translates to what molecular clock rate? Make sure to include your units.

1 nucleotide base pair difference per 1000 years

______is a public data bank that has literally billions of sequence records, and the sequences are for lots of different taxa. If someone has figured out what a sequence similar to one you are studying does in say bacteria, e.g., whether it affects cell division or metabolism, etc., the data base also links to that information. When sequences match pretty closely for very distantly related taxa, e.g., bacteria and animals, we would say the sequence is _______________ (from the list of terms at the top).

GenBank ; conserved

Your________with your sibling is your parents, with your cousins is the grandparents that you share.

MRCA (most reason common ancestor

_____is the general idea that when evidence points equally strongly to a complex and a simple explanation, you go with the______ one.

Maximum Parsimony; most simple

If we want to determine evolutionary relationships, i.e., who descended from whom, i.e., who is most closely related to whom, would it be okay to measure lots of characters and assume the taxa that are most similar on average are most closely related?

No

Within the human genome (all the DNA in the chromosomes in a person) does all DNA have a detectable biochemical effect?

No

_______are traits that are useful in creating phylogenies because more than 1, but not all, taxa being put into the phylogeny have the trait.

Shared Derived Characters

is the study of classification of organisms into named classification groups, i.e., into _____taxa, such as Hominidae, Chordata.

Taxonomy

How is generating a molecular clock useful? I.e., what are they used for?

estimating time since divergence, i.e., since MRCA

If the line for C was shorter than it is in the below diagrams, it would tell you that taxon C is

extinct

Where did it come from, i.e., the HIV currently found in humans share a common ancestor with the HIV found in _____

certain primates

_______is a group of taxa that includes their common ancestor and all that ancestor's descendants. The adjective that describes such a group is________

clade; monophyletic

In creating monophyletic taxa, i.e., ____________, we purposely pick not just the taxa that we want to make a phylogeny for, but also a taxon that we know is not super-closely related, i.e., a(n) _________, to serve as a reference point. We use this along with fossil information to determine which traits are older versus more recent, i.e., to ______ the tree.

clades; outgroup; root

It has been thought that DNA without a detectable biochemical effect should be best as a molecular clock, i.e., may meet the assumption that the rate of change of the DNA is ________

constant

Using a molecular clock assumes what about the rate of change in molecules - that it is constant or not?

constant

The opposite of an ancestral trait is a ________trait.

derived

Computers use mathematical algorithms (rules) such as __________ ____________ to generate & pick phylogenies.

maximum parsimony

Any unit, e.g., miles, volume, number, etc., per time is called a(n) _______.

rate

You are interested in a constant rate; rate is defined how in terms of x and y axis? __________ so X axis must be?________

rate is per something, usually time. It is the slope, i.e., rise over run, i.e., change in y over change and x, ; time

What is it called when you figure out where the base, the ancestor, of an entire phylogeny is?

rooting a tree

Do you have a more recent common ancestor with your sibling or your cousin? ____

sibling

Would you want to collect data from types of DNA that are usually fast evolving or slow evolving if you want to determine relationships at a more inclusive taxonomic level, e.g., phyla (vs say species)?

slower evolving [slower substitution rate of nucleotides]

Although the term that scientists use is molecular clock, one might argue that the term molecular clock is better for quickly evolving DNA like that in mitochondria and molecular calendar is better for what?

slowly evolving DNA [like in rDNA]

Which 4 of the following trees show the same evolutionary history for taxa A, B, C, and D?_______

1st & 2nd & 4th & 5th

_______is the rate at which traits, e.g., nucleotides (A, T, G, C) are chaning over time, and it is used to estimating time since divergence of two groups of taxa from a MRCA.

A molecular clock

Looking at the left-most phylogeny above, which 3 of the following 8 groups (choices) could be a clade and hence monophyletic?

As long as you included the farthest back where they all connect, i.e., their MRCA

What other molecular characters could be used besides the nucleotides (A,T,G,C) in sequence(s) of DNA?

DNA RNAamino acidsproteins, so use the nucleotides [A,T,G,C] in sequence(s) of DNA or the nucleotides [A,U,G,C] in sequence(s) of RNA or amino acids or proteins

Phylogeneticists often refer to phylogenies as hypotheses because all scientific conclusions are based simply on the preponderance of __________, and they know that their evidence is incomplete because new ________ or ______ may be discovered

Evidence; theories; or extant species

The latter is in terms of requiring the fewest what?

Evolutionary changes;

The characters chosen to reconstruct phylogenies should be _____________ (not analogous) because only the former reflects ___________ , and the characters should be __________ not ancestral, i.e., the character should generally be present in more than 1, but less than all, taxa.

Homologous; common ancestry; shared derived

Do all types of DNA generally evolve at the same rate? no, some faster than others How is the answer relevant to creating phylogenies?

Phylogeneticists often want to estimate the date when the MRCA of 2 taxa was. If it was likely a short time ago, then you need to use genes that changes relatively quickly. [If it changes really slowly, it would be like using a clock with only an hour hand to measure milliseconds.]. If divergence was likely a long time ago, then genes that change slowly will work better.

If 20 amino-acid differences between humans and cows in a globin protein and our last common ancestor was 100 million years ago. This rate of divergence appears to be constant in all vertebrates (fish, mammals..). Carp and shark (both fish) differ by about 10 amino acids. How long ago did carps and sharks diverge? [These numbers may not be biologically accurate.]

The clock is 20 amino acid difference per 100 million years. Carp and shark have 10 a.a. differences. I want my answer to be in time, i.e., years. To get those units on top, I need to divide by 20 aa diffs per 100 million years. To cross out the aa diffs, it is 10 aa diffs that I need to divide. Thus, 10 aa diffs divided by 20 aa diffs per 100 million years, which is the same as 10 aa diffs multiplied by 100 million years per 20 aa diffs, which is 10*100 million years divided by 20 = 50 million years. Another way to approach would be to say 20 amino acid difference per 100 million years reduces to 5 million years for every 1 amino acid difference, and since there are 10 aa diffs between carp and shark, that is 50 million years

Can a clade be any taxonomic level, e.g., a Kingdom?___ a phylum, ....?_____ Thus a clade can be a domain or KP_______

Yes ;_Class _Order _Family _Genus _Species.

In each case, who is the ancestor (not their name, rather their relationship to you (parents, grandparents, ...)?

Your MRCA (most recent common ancestor with your sibling is your parents, with your cousins is the grandparents that you share.

Phylogeneticists study characters of organisms (e.g., morphological or molecular characters) to decide which species should be placed in the same genus and which genera should be placed in the same ____________

family, or supergenera or subfamily, etc. DKPCOFGS, sub = part of (under), super = contains multiple (above)

Hint 1: Logic: Imagine creating a phylogeny of 3 different-looking prokaryotes that you found. Three problems with just looking at overall similarity are 1) In determining relatedness, does it matter what media each type of bacteria grew on? yes I.e., is phenotype or genotype going to be better?

genotype, and if the 3 are all grown under the same environmental conditions, then any differences are differences in genotype

Which traits should be used, homologies or analogies, or does it not matter?

homologies, NOT analogies, because only homologies reflect common ancestry, and patterns of MRCA is what a phylogeny is

To the best of our knowledge, has HIV always infected humans, or at least as far back as we have data for?

it has not

Constant means the relationship between x and y is not changing, i.e., a constant slope is a straight ______

line

If you know the taxonomy for the species in a group, e.g., for the Galapagos finches, do you know which species are most closely related?

maybe, generally species in a given taxon are more closely related than those that are in the same taxa that is of a more inclusive classification level

A clade is a(n) _____________________group.

monophyletic

what are 4 other processes by which a character may evolve?

mutation, gene flow, random genetic drift, nonrandom mating

Or if you are looking at DNA sequences, you could be more specific in terminology, and say the fewest _________

mutations

Are unshared characters useful? E.g., if 1 bacteria is red, 1 is blue and 1 is yellow, does this help see which 2 are more closely related? (yes or no)

no

Would the answer be different for RNA base pairs per year than for DNA base pairs per year? Nucleotide per year? for amino acids?

no, because each triplet DNA code is translated to a triplet RNA (e.g., the DNA codon AGT is translated to the RNA codon AGU] ; no, because the term nucleotide and base or base pair are used almost interchangeably [If you think of DNA as a twisted ladder, a nucleotide consists of a single base pair rung with its part of the sugar-phosphate backbone on either side] ;yes, divide the number of DNA (or RNA) bases (or base pairs) by 3, because each triplet of bases codes for 1 amino acid

Y axis might be number of differences in DNA or __________ (since if you know this, you know DNA) or __________ (since if you know this, you have a good idea of DNA) .

number of differences in RNA; number of differences in amnio acids

Imagine you know a DNA nucleotide base pair has changed at a particular locus over 100 generations from the DNA nucleotide adenine (A) to the DNA nucleotide guanine (G), it might have changed just once; or it might have changed back and forth, so it might have changed multiple times. How many times would you assume it changed if you were using the idea (or law or principle) of parsimony?

once

When creating a phylogeny, a taxon that is known to be less closely related to the other taxa and so can be used to root the tree, is a(n)______________

outgroup or basal taxon

One mathematical method of choosing among alternative phylogenies is maximum __________.This method picks the phylogeny that is most ______________.

parsimony ; simple;

If a given sequence of DNA has no detectable biochemical effect, that means that it has no effect on anything that humans can see, i.e., no effect on the _____________ ; and if it has no effect on that, it has no effect on ____________ , e.g., number of offspring produced, and so is not influenced by what evolutionary process? Does that mean it cannot evolve? (yes or no)

phenotype; fitness; natural selection; no

Phylogeneticists often also create trees, like those below, i.e., ____________________, which reflect what

phylogenies ; the pattern of most recent common ancestors

So, __________________ = family trees but covering MUCH more time, a maximum of ________ of years sometimes (hundreds, thousands, millions, billions or infinity?). (Hint: the earth is roughly how old)

phylogenies; billions

If units are given, the length of the lines in phylogenies are meaningful; specifically, the lengths might be calibrated in terms of what 2 basic types of information?

time or amount of genetic change, e.g., number or % of DNA base changes

Why don't phylogeneticists use computers instead of doing it by hand?

too many possible trees once you start looking at more than a few taxa; and it is best to use many characters to get an accurate tree and figuring out how many minimum genetic changes there would be for each character for each tree is a lot

Phylogeneticists also use only shared derived characters. If all the taxa we are studying have a trait, it is "ancestral." Are such characters useful, e.g., if all the bacteria are cocci, does this help you decide which 2 are more closely related than the 3rd?

traits that every taxon in your phylogeny have don't help show which 2 of the 3 taxa have a MRCA

In contrast, if just a subset of 2 taxa have the trait, e.g., just 2 are cocci, it would be called a derived character. Are derived characters useful?

yes, especially if more than one taxon has it

Is there DNA within your cells in any place other than the nucleus?

yes, in your mitochondria