Download Chapter 16 Practice Problems

Chapter 16
Practice Problems
16.1 What are the three hierarchical levels of biodiversity recognized by the IUCN? Name two
additional organizational levels. Is any particular level most important to focus conservation
efforts? Why or why not?
16.2 Name three temporal aspects of biodiversity conservation. Which is most important and
should have the greatest priority? Explain your answer.
16.3 Describe several scenarios and evolutionary processes that can lead to isolated populations
failing to show reciprocal monophyly of DNA lineages.
16.4 What are the three main schools of taxonomic classification? Which school is a
combination of the other two? Which is most widely used today? Which is most appropriate for
studies of evolutionary history?
16.5 The figure below shows a phylogenetic tree (for three alleles x, y, and z derived from the
ancestral allele w) and the map of geographic areas in which the alleles are distributed (modified
from Moritz and Faith 1998). Conduct a phylogeographic analysis using (a) and the geographic
distributions of alleles shown in (b) and (c). When overlaying the phylogeny on to each of the
two hypothetical spatial distributions, is there evidence for phylogeographic structuring? Why or
why not? Which spatial distribution reveals stronger phylogenetic structuring?
16.6 What is an ESU? What are the main principles and common criteria used for ESU
identification?
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16.7 (a) How do we define a management unit (MU)? (b) How does a MU differ from an ESU?
(c) How might molecular genetic markers (e.g., microsatellites or SNPs) be used to help identify
MUs?
16.8 (a) What different kinds of information should be used when identifying or delineating
units for conservation? (b) Why is it important to use different kinds of information?
16.9 What are the potential advantages and disadvantages of using adaptive gene markers for
identifying ESUs?
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Assignment Problems
16.10 Define paraphyly and polyphyly. Does our currently-accepted classification of reptiles
(considering birds) represent an example of paraphyly or polyphyly? Are reptiles monophyletic
in our currently-accepted classification (Figure 16.3)?
16.11 It is increasingly feasible to use individual-based approaches to describe the genetic
relationships among populations (Section 16.4.1).
(a) Explain how we might wrongly infer that a genetic discontinuity (partial barrier to gene flow)
exists between sampling locations if only one local clusters (i.e., group) of individuals is sampled
from each of two distant locations in a continuously distributed population (see Figures 9.8, 9.10,
and 16.13).
(b) Briefly explain how could this kind of erroneous “barrier” inference be avoided?
16.12 (a) Explain why high gene flow among MUs makes it challenging to identify MUs when
using molecular genetic markers.
(b) Explain why FST values alone are not particularly useful and potentially misleading when
identifying MUs (Hint: Nm; equilibrium; Table 16.4).
16.13 (a) Using the four sequences below, build a parsimony network by hand by connecting the
sequences in a branching network with four terminal nodes, i.e., sequences, as in Figure 16.6b or
16.14a.
(1) gagtattata agggcgagtg tcatttcttc aacgggaccg
(2) gagtatgcta agagcgagtg tcgtttcttc aacgggacgg
(3) gagtatgata agagcgagtg tcgtttcttc aacgggaccg
(4) gagtatgcta agagcgagtc tcgtttcttc aacgggacgg
(b) BLAST (Basic Local Alignment Search Tool), is an algorithm for comparing DNA
nucleotide sequence information (or amino-acid sequences). A BLAST search enables a
researcher to compare a query sequence (e.g., above) with a database of sequences, and identify
a list of sequences that resemble the query sequence. For example, after the discovery of a
previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the
human genome to see if humans carry a similar gene. Also, after discovery of a RAD-tag
sequence associated with a fitness trait (e.g., in a natural population of fish or wildlife), a
scientist will often BLAST the sequence to see if it falls in or near a gene in a related species that
has a full genome sequence.
Conduct a nucleotide BLAST search (http://www.ncbi.nlm.nih.gov/BLAST/) with the sequence
number (1) from above to identify the gene and species of origin of the sequence.
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Once you are on the NCBI blast page (http://www.ncbi.nlm.nih.gov/BLAST/), under “Basic
BLAST”, choose (click on) “nucleotide blast”. Remove the three white spaces in the sequence
when you paste the sequence into the large window under “Enter accession number(s), gi(s), or
FASTA sequence(s)”. Click on the “BLAST” button, and have fun (a blast) while you wait for
the results.
16.14 (a) What is the minimum number of adaptive gene markers that should be used to identify
adaptively-differentiated populations?
(b) If many genes (or exons) could be sequenced, what proportion of the exome (e.g., 25,000
coding genes) should be sequenced in order to reliably identify ESUs?
(c) Describe a simple study design to empirically estimate the number of genes that must be
sequenced to reliably identify adaptively-differentiated populations. (Hint: Choose a species for
which adaptively-differentiated populations are already well defined and for which thousands of
markers exist, e.g., stickleback fish in Guest Box 8).
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