The following are among many review articles on
certain aspects of phylogenetic methods and
uses in biology:
Model selection in phylogenetics, by J. Sullivan
and P. Joyce (Annu. Rev. Ecol. Evol. Syst. 36:
445–460, 2005).
Phylogenetic inference using whole genomes,
by B. Rannala and Z.-H. yang, (Annu. Rev. Ge-
nomics Hum. Genet. 9: 217–231, 2008).Evolutionary inferences from phylogenies: a re-
view of methods, by B. C o’Meara (Annu. Rev.
Ecol. Evol. Syst. 43: 267–285, 2012).
High-throughput genomic data in systematics
and phylogenetics, by E. M. lemmon and A.
R. lemmon (Annu. Rev. Ecol. Evol. Syst. 44:
99–1 21 , 201 3).
Animal phylogeny and its evolutionary implica-
tions, by C. W. dunn, g. giribet, g. d. Edge-
combe, and A. Hejnol (Annu. Rev. Ecol. Evol.
Syst. 45: 371–395, 2014).PRoBlEMS ANd dISCUSSIoN ToPICS
- What is the evidence that incomplete lineage
sorting (IlS) has affected dNA variation in
humans, chimpanzees, and gorillas? How could
the authors of the study described in Scally et al.
2012 (Nature 483 [7388]: 169–175) tell that IlS had
occurred? - With improving technology, acquiring dNA
sequences from different organisms becomes
easier each year. With that in mind, some authors
(e.g., Scotland et al. 2003, Systematic Biology
52 [4]: 539–548) have suggested that the use of
morphological data is less important than dNA
sequence data and have called for less emphasis
on the use of comparative morphology in build-
ing phylogenies. other authors maintain that
despite the explosion of molecular data avail-
able, morphology still has an important role in
phylogenetics (for examples, see Wiens 2004,
Systematic Biology 53 [4]: 653–661 and Will and
Rubinoff 2004, Cladistics 20 [1]: 47–55). What
are the reasons for and against using morpho-
logical data in phylogenetic reconstruction?
When might morphological data be especially
important? - A heated debate arose in the mid-twentieth
century: some systematists insisted on the iden-
tification of monophyletic groups to reconstruct
phylogeny and use those for classification or
taxa based on their relatedness. others placed
organisms into taxonomic groups based sim-
ply on overall morphological similarity (using
algorithms in an attempt to remove subjectivity
from classification). The major difference in the
approaches is that the first uses only apomorphic
(derived) characters in its analyses, whereas the
second does not distinguish between apomor-
phic and plesiomorphic (ancestral) characters,
because measuring total similarity is the goal.
discuss how this difference in use of characters
might result in discrepancy in classification.
Which approach is more common today?- If a branch on a phylogeny shows few changes
in sequence, we can assume that changes are
rare, so mutations are unlikely to affect the same
nucleotide position more than once. If a branch
is “long,” with many changes to sequence, mul-
tiple mutations at the same nucleotide locus are
more likely. How might this mislead researchers
working on phylogenetic reconstruction? (Hint:
one common complication of this type is called
“long branch attraction.”) How is this related to
the saturation of the curve showing sequence
divergence of the third positions in codons in
figure 16.5? - Parsimony, maximum likelihood, and Bayesian
inference are different analytical techniques for
developing phylogenies from dNA sequence
data. Why would a researcher choose one
method over another? What are the advantages
and disadvantages of the three methods? - What should a biologist do if she finds that dif-
ferent methods of analyzing the same data (say,
parsimony and maximum likelihood) provide
different estimates of the relationships among
certain taxa? What should she do if the differ-
ent analytical methods give the same estimate,
but the estimate differs depending on which of
two different genes has been sequenced? (Hint:
your answers do not depend on knowing how
maximum likelihood works.)
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