Download LS50B Concept questions: end of section 6: Solutions

LS50B Concept questions: end of section 6: Solutions
April 22, 2016
Concept questions
These are some warm up/concept questions from the part of section 6 that doesn’t have a problem set,
as well as a few extras from earlier parts of section 6. There will not be a warm up style problem on the
midterm, but it may be helpful to review these questions and be sure you understand the material well
enough to answer them.
1. Why is it important to know whether the Porifera-sister hypothesis or the Ctenophore-sister hypothesis
is correct? In other words, how would it change our conclusions about animal evolution if one or the
other were correct?
Solution: Knowing whether sponges or ctenophores are the sister species to all other animals would
allow us to draw conclusions about the series of events that took place in the evolutionary history of
all animals. Specifically, if the Porifera-sister hypothesis is correct, it would support the idea that the
most recent common ancestor of all extant metazoans was an animal with a relatively simple body plan
(more similar to current sponges). If instead the Ctenophore-sister hypothesis is correct, that would
suggest one of two things: either that the most recent common ancestor of all extant metazoans may
have had a more complex body plan than was previously believed, and that some of that complexity
was lost in the ancestor of the Porifera, or that some aspects of the biology of Ctenophores and other
non-sponge metazoans may have evolved multiple times.
2. Define: taxon; clade; monophyletic group; polyphyletic group; paraphyletic group.
Solution:
• A taxon is any grouping of organisms according to some characteristic. A taxon may or may not
suggest anything about the evolutionary relationships or organisms in the taxon. (Note: a taxon
can include a single species or multiple species).
• A clade and a monophyletic group are two ways of referring to a common ancestor of some
group of organisms and all of the descendants of that single common ancestor.
• A polyphyletic group is a group of organisms that do not have their most recent common
ancestor in common (i.e. at least one of them has a sister clade that’s not in the group).
• A paraphyletic group includes a given common ancestor and some, but not all, of its descendants.
3. Why should we care, from a scientific perspective, about resolving phylogenetic trees? Why is it useful
to classify organisms according to their biological characteristics? Name at least two reasons.
Solution: Classifying organisms according to their biological characteristics and resolving phylogenetic
trees is required to both generate and test hypotheses about the evolutionary history of specific traits
that we are interested in. It can also help us recognize and study unusual or unexpected events such
as horizontal gene transfer.
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4. Why might a scientist choose to use a well-studied model organism? Why might a scientist choose to
work in a non-model system?
Solution: Different model organisms are useful for different types of scientific studies, because many
tools have been developed that makes certain types of experimental tests possible in some model
organisms but not in other organisms and because they have been chosen for certain characteristics
that make them amenable to rearing in the lab. However, model organisms represent only a very tiny
fraction of the diversity of life on earth, and many scientists choose to work with non-model organisms.
This can be a good choice if, for example, they are interested in a characteristic that is not found in
any model organism or if they are interested in understanding evolution by studying a large set of
related organisms.
5. What is a Hox gene?
Solution: Hox genes are a specific group of transcription factors involved in specifying the body plan in
animals. They all contain a homeobox domain that binds to DNA (Note: not all homeobox-containing
transcription factors are Hox genes, but all Hox genes have homeobox domains). They are often found
in clusters within the genome, and within the cluster the linear order on the chromosome corresponds
to the spatial order in which they are expressed during development and in some organisms, also to the
temporal order of expression. Hox genes are not necessary for the existence of certain regions but are
instead involved in specifying the identity of the regions, such that misexpression or loss of function of
Hox genes results in body regions incorrectly taking on traits typically associated with other regions.
6. In what way are the Hox genes an example of a conserved evolutionary module?
Solution: The Hox genes function very much in the way described in the answer to the previous
question throughout many diverse taxa of animals. Although the anterior of a fruitfly and the anterior
of a mouse look very different, the module responsible for determining the anterior - posterior identity
of various body regions is conserved.
7. What is an ortholog? What is a paralog? Why is it important to know which you are dealing with
when constructing a phylogenetic tree?
Solution: Orthologs are genes found in different species that derived from a common ancestor sequence; paralogs are genes found in a single species that derived from a common ancestor sequence.
When using genetic information to build a phylogenetic tree, it is important to figure out which genes
are orthologs and which genes are paralogs, because it will affect the number of independent comparisons you are actually making in your tree. For instance, take a look at the following diagram: In the
left (pink) tree, the human A gene family is orthologous to the zebra A gene family, but human A1,
A2, and A3 are parallels and zebra A1, A2, and A3 are paralogs. If we measure divergence between
human and zebra A1, human and zebra A2, and human and zebra A3, we are not measuring three
divergence events: we are measuring a single divergence (in the ancestral A gene that was present in
the common ancestor of human and zebra) three times. However, in the right (purple) tree, human and
zebra A1 are orthologs; human and zebra A2 are orthologs; and human and zebra A3 are orthologs:
each of these pairs was derived from a single one of a set of paralogs that were present in the common
ancestor of human and zebra. In this case, measuring divergence between human and zebra A1, human
and zebra A2, and human and zebra A3 actually does measure three independent events.
8. What is horizontal gene transfer? What kind of evidence would suggest that a horizontal gene transfer
event has taken place?
Solution: Horizontal gene transfer is the transfer of genetic information between organisms from
different species, as opposed to vertical gene transfer which is more typical inheritance of genetic
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information through common descent. Some evidence that a sequence could be a result of horizontal
gene transfer includes: a different GC content or codon usage from the rest of the genome (if the
transfer was recent); phylogenetic analysis grouping the horizontally transferred sequence as most
closely related to a distant species while the rest of the genome clusters with a different set of organisms;
and evidence that would support a possible mechanism for the horizontal gene transfer to have occurred
(e.g. evidence of past endosymbiosis between the donor and recipient).
9. What are two possible reasons why different scientists could start with the same genetic information
and end up with different phylogenetic trees?
Solution: It is fairly common for different groups of scientists to analyze the same genetic data
but come to different conclusions. Some reasons might include that they used different models for
constructing the phylogenetic trees (each of which has its own strengths and weaknesses), or that one
group decided that some parts of the dataset represented real useful information and another group
concluded that those parts of the data were likely due to artifacts or contamination.
10. What might cause an evolutionary constraint on particular types of adaptation? Give one example of
an experiment that found evidence either for or against constraint acting in a particular system.
Solution: Often it’s the case that for various reasons not all theoretically beneficial adaptations are
possible for a particular organism. These reasons might include shared developmental mechanisms
between different aspects of an organism’s phenotype, or groups of mutations that would have to
occur simultaneously if they were to be beneficial rather than deleterious. One experiment that found
evidence for constraint on butterfly wing spot development was the experiment where scientists tried
to select for different color phenotypes in different wing spots and found that they were not able to
select for opposite color phenotypes in different spots. One experiment that found evidence against
constraint was done by the same group, when they selected for the same or different sizes of different
wing spots, and found that they could evolved butterfly populations with any combination of large and
small spots.
11. There are many distinct species of tree shrews in a particular forest. Some species are diurnal (meaning
they are most active during the day) and some are nocturnal (they are active at night). You notice
that all of the diurnal tree shrews have lighter colored fur, longer fur, and smaller eyes than all of the
nocturnal species. What can you conclude about what traits selection has acted on in tree shrews?
Solution: Absolutely nothing! (At least based on this evidence alone). Think about the red/small
balls cartoon. It could be that selection acted on all three of these traits independently; that selection
acted on one of them and the others are either pleiotropic or genetically linked; or that selection acted
on some other phenotype that you haven’t measured but is linked with some or all of the observed
phenotypes. Put another way, you might conclude that there may have been selection of lighter color,
longer fur, and smaller eyes, but you cannot conclude from this information anything at all about what
there may have been selection on.
12. What is an evolutionary arms race? Describe one example.
Solution: An evolutionary arms race is when changes in a trait in one organism result in selection for
changes in some trait in another organism because of the way the two organisms interact. For example,
there may be simultaneous selection for parasites to develop ways to avoid being recognized by the
host’s immune system and simultaneous selection for hosts to better recognize the same parasites,
which could lead to a rapid divergence in both host and parasite phenotype. As another example, Ben
talked about the possibility of an arms race that resulted in the simultaneous development of hard
teeth in predators and hard shells in prey.
13. In a diploid organism, it is possible to define dominance as a kind of epistasis between the two alleles
present at a single locus in a single individual. Imagine a single locus with two alleles: A, which is fully
dominant, and a, which is recessive. Define the relative fitness of a recessive homozygote as w=1, and
assume that individuals with the dominant phenotype leave on average 1.05 times as many offspring
as individuals with the recessive phenotype.
• What is the selective coefficient, sA , of the A allele? Solution: sA =0.05, since waa = 1 and
wAa =wAA =1.05.
• What is the selective coefficient, sa , of the a allele? Solution: sa = 0
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• What is the epistatic coefficient δAA of two A alleles? Solution: δAA = -0.05. This means that
waa = 1; wAa = 1 + 0.05; and wAA = 1 + 2 ×sA + δAA = 1 + 0.1 - 0.05 = 1.05.
14. Name and explain two advantages and two disadvantages of experimental evolution.
Solution: Advantages: we can repeat the same evolution experiment many times, and we can control
the conditions (e.g. population size, frequency and size of bottlenecks; conditions of selection; starting
phenotypic and genotypic variance). Both of these factors mean that we can better understand the
general rules governing evolutionary processes. Disadvantages: we can only evolve so many generations,
and the conditions are so artificial that it may be difficult to determine how to translate findings from
experimental evolution to understanding much more complex natural systems.
15. You calculate dN/dS for your favorite gene in two related species. What does each of the following
values of dN/dS suggest about selection on the gene, and why? dN/dS >> 1; dN/dS ≈ 1; dN/dS <<
1.
Solution: dN/dS is the ratio of the proportion of possible amino-acid altering mutations have happened, to the proportion of possible synonymous mutations that have happened. Values of dN/dS ≈
1 suggests that there is no distinction between mutations that do and do not alter the amino acid
sequence of a particular protein, and that there has been neither selection for nor against changes in
amino acid sequence. dN/dS << 1 suggests purifying selection (selection against most mutations that
change the amino acid sequence) while dN/dS >> 1 suggests selection for mutations that change the
amino acid sequence.
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