Evolution, 4th Edition

■■Phylogenetic relationships can be difficult to

determine, and for this reason often require

data on many characteristics, such as extensive

dNA differences among species. one of the

main reasons a phylogeny could be wrong is the

repeated, independent evolution of a base pair

or other character state by convergent, parallel,

or reversed evolution.

■■Phylogenies are especially difficult to de-

termine if successive branching events were

closely spaced in time, because few evolution-

ary changes are fixed during short intervals.

A related problem is incomplete lineage sort-

ing, resulting in gene trees that differ from the

species tree that one may be trying to estimate.

yet another difficulty is introgression caused by

hybridization (or horizontal gene transfer).

■■A variety of methods are used to estimate

phylogenies. The simplest is parsimony, a rule

that chooses whichever phylogenetic tree re-

quires the fewest evolutionary changes. other

methods choose among the different possible

phylogenies based on their likelihoods or prob-

abilities. Methods differ in their strengths and

weaknesses, and in the kinds of data they can

analyze. In many cases, different methods return

very similar results.

■■Branching events in phylogenies can often be

dated approximately, using dNA sequence

differences that approximately conform to a

geologically calibrated molecular clock. The rate

of sequence evolution varies among parts of the

genome and among clades, and can sometimes

vary within clades. Tests are always necessary to

confirm rate constancy. The causes of rate differ-

ences among groups of organisms are uncertain.

■■Phylogenies are useful for inferring histories of

genes and other historical changes, such as in

human cultures and languages.

■■An important use of phylogenies is tracing the

history of evolution of characteristics, through

ancestral state reconstruction. This approach has

been used to synthesize ancestral dNA sequenc-

es and proteins, to better understand how their

functions have evolved.

■■The comparative method uses convergent

evolution to test hypotheses about adaptation.

Statistical tools use the phylogeny to control for

the effects of shared ancestry.

■■In modern systematics, classification of organ-

isms is based on their phylogeny. In an ideal

classification, each named taxon is monophy-

letic, including all the species thought to be

descendants of a single common ancestor. The

classification consists of nested, named mono-

phyletic groups. Such a classification reflects

evolutionary history and usually conveys a great

deal of information about the species.

TERMS ANd CoNCEPTS

ancestral

Bayesian inference

clade

convergent

evolution

crown group

derived

evolutionary

reversal

gene tree

homoplasy

incomplete lineage

sorting (ILS)

likelihood

monophyletic

group

most recent

common ancestor

(MRCA)

outgroup

paraphyletic

parsimony

polyphyletic

relative rate test

stem group

synapomorphy

SUggESTIoNS foR fURTHER REAdINg

Tree Thinking: An Introduction to Phylogenetic Bi-

ology, by d. A. Baum and S. d. Smith (Roberts

and Company, greenwood village, Co, 2012),

is a comprehensive introduction to the con-

cepts, methods, and uses of phylogenetics in

biology, for nonspecialists.

Molecular Systematics, edited by d. M. Hillis, C.

Moritz, and B. K. Mable (Sinauer Associates,

Sunderland, MA, 1996), is outdated in some

ways, but is still a very useful, comprehensive

introduction to some molecular methods and

analytical procedures that are still used.

for deep coverage of phylogenetic analysis,

see Inferring Phylogenies, by J. felsenstein

(Sinauer Associates, Sunderland, MA, 2004).

The most recent synthesis of phylogenetic stud-

ies into a single tree of life is “Synthesis of

phylogeny and taxonomy into a comprehen-

sive tree of life” by C. E. Hinchliff, S. A. Smith,

J. f. Allman, and 19 others (Proc. Natl. Acad.

Sci. USA 112: 12764–12769, 2015).

SUMMARy

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