Practice Problems s2

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?

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?

1 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?

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

2 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.

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

3 populations are already well defined and for which thousands of markers exist, e.g., stickleback fish in Guest Box 8).