Evolution, 4th Edition

SUGGESTioNS foR fURTHER READiNG

Tree Thinking: An Introduction to Phylogenetic

Biology, by D. A. Baum and S. D. Smith (Rob-

erts and Company, Greenwood Village, Co,

2 012), is a comprehensive introduction to the

concepts, methods, and uses of phylogenetics

in biology, for non-specialists.

These journal articles provide introductions to

some of the topics in this chapter:

omland, K. E., L. G. Cook, and M. D. Crisp. 2008.

Tree thinking for all biology: The problem with

reading phylogenies as ladders of progress.

BioEssays 30: 854–867.

Bromham, L., and D. Penny. 2003. The modern

molecular clock. Nat. Rev. Genet. 4: 216–224.

Pagel, M. 1999. inferring the historical patterns

of biological evolution. Philos. Trans. R. Soc., B

352: 519–529.

PRoBLEMS AND DiSCUSSioN ToPiCS

1. Suppose species 1, 2, and 3 are endemic to a
   group of islands (such as the Galápagos) and are
   all descended from species 4 on the mainland
   (which will serve as an outgroup; its very large
   population size means that no new mutations
   have become fixed in its population in the time
   since the islands were colonized). We sequence
   a gene and find ten nucleotide sites that differ
   among the four species (among many other loci
   that do not vary). The nucleotide bases at these
   sites are
   Species 1: GCTGATGAGT
   Species 2: ATCAATGAGT
   Species 3: GTTGCAACGT
   Species 4: GTCAATGACA
   Estimate the phylogeny of these taxa by plot-
   ting the changes on each of the three possible
   unrooted trees and determining which tree
   requires the fewest evolutionary changes.


2. Suppose the species in the previous question
   are birds that differ in diet: species 1 and 3 are
   insectivorous (they eat insects), and species 2
   and 4 are frugivorous (they eat fruit). We also
   happen to know that another frugivorous spe-
   cies, species 5, is a mainland relative of species
   4. Given your best estimate of the phylogenetic
   history, what has been the probable history of
   the evolution of diet in this clade of birds?


3. Phylogenetic information is the basis for describ-
   ing patterns of evolution, yet some examples of
   patterns were presented without phylogenetic
   trees in the text. Consider the following exam-
   ples and discuss what phylogenetic evidence

or inference was left unstated: (a) The fusion of

hindlimb bones during embryonic development

of birds is a derived trait, not an ancestral trait,

relative to the unfused condition in crocodiles.

(b) Pentadactyly (five digits) is homologous in

humans and crocodiles. (c) The sting of a wasp

is derived from an ovipositor but is modified in

both structure and function. (d) insects evolved

wings, but the character was lost for many wing-

less insect groups. (e) frogs have some traits that

are very similar to those of their deep ances-

tors (five toes on the hindlimb, multiple bones

in the lower jaw) but others that are relatively

advanced (lack of teeth in the lower jaw).

4. There is evidence that many of the differences in
   DNA sequence among species are not adaptive.
   other differences among species, both in DNA
   and in morphology, are adaptive (as you will see
   in Chapters 3, 5, and 7). Do adaptive and non-
   adaptive variations differ in their usefulness for
   phylogenetic inference? Can you think of ways in
   which knowledge of a character’s adaptive func-
   tion would influence your judgment of whether
   or not that character provides evidence for rela-
   tionships among taxa?


5. it is possible for two different genes to imply
   different phylogenetic relationships among a
   group of species. What are the possible reasons
   for this? if there is only one true history of forma-
   tion of these species, what might we do in order
   to determine which (if either) gene accurately
   portrays that history? is it possible for both phy-
   logenetic trees to be accurate even if there has
   been only one history of species divergence?

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