Chapter 2
THE TREE OF LIFE:
CLASSIFICATION AND PHYLOGENY
Summary of Chapter 2: EVOLUTION, D. Futuyma, 2nd Ed., 2009.
We have grouped organisms for easier study by comparing similarities and differences.
CLASSIFICATION OR TAXONOMY is the ordering of organisms into groups. It includes the
principles procedures used in classification.
PHYLOGENY: refers to the evolutionary history of a species or group of species in terms of
their derivations through evolutionary processes; which species share a common ancestor, which
species share a more distant ancestor, etc.
SYSTEMATICS: the classification of organisms using phylogenetic relationships. It includes
comparative anatomy, comparative biochemistry, comparative physiology, etc.
Systematics is the study of biological diversity and evolutionary history of organisms. It uses
phylogenetic trees to show the evolutionary relationship of organisms.
Systematics includes...

Taxonomy, the science of identifying and classifying organisms.

Phylogenetics, the study of the evolutionary history of organisms.

Nomenclature, the system used in naming organisms.
CLASSIFICATION
The present system of nomenclature was devised by Carolus Linnaeus (Carl von Linné), a
Swedish botanist who lived in the 18th Century.
Linnaeus published in 1753 a book called Species Plantarum, "the kinds of plants".





Binomial system of nomenclature: Genus + species epithet = scientific name of the
plant.
Hierarchical classification: groups within groups.
The levels of classification are referred as taxonomic categories, e.g. phylum, class.
A particular group of organisms is called a taxon.
Taxonomy is hierarchical: taxa are grouped into broader taxa.
Species are grouped into genera (sing. Genus).



Genera into families; families into orders; orders into classes; classes into divisions;
divisions into kingdoms.
There are intermediate taxonomic categories, e.g. superfamily or subspecies.
Higher taxa are those above the species level.
Since Darwin, most systems of classification attempt to reflect phylogenetic relationships.
It is difficult to find an unbroken line of ancestors that connect the different groups in questions.

Natural processes often destroy fossil evidence.
Taxonomists have to weigh the evidence provided by similarities between organisms.
Darwin wrote On the Origin of Species in 1859.
Darwin proposed that on occasion, a species may split into two species, which at first are very
similar to each other but with time diverge, become more different.
Each of these two species may in turn split into two other daughter species, and so on.
Closely related species are descended from a relatively recent common ancestor (monophyletic);
distantly related species are descended from a more remote ancestor, farther back in time.
In Darwin’s words, all species extant and extinct form the Great Tree of Life, a phylogenetic
tree.
A phylogenetic tree shows monophyletic groups and their common ancestor.
Phylogenetic trees are proposed based on the characteristics shared by the taxa.
They represent evolutionary relationships.
Darwin’s hypothesis proposes that a hierarchical classification should reflect a historical process
that produced organisms with true genealogical relationship: phylogeny.

Classification should reflect the real history of evolution.
INFERRING PHYLOGENETIC HISTORY
Similarity and common ancestry
A feature or a trait is called a character.


A character may be a morphological characteristic, e.g. presence of hairs, shape of shell,
etc.
A character may also be a trait at the cellular, biochemical or molecular level, e.g. a
particular nucleotide sequence.
A character may have several character states, e.g. white or purple flowers, hairs long or short,
“A” base or “C” base in a particular nucleotide sequence.

Ancestral or plesiomorphic characters are found in the common ancestor of daughter
species.
o
http://wordinfo.info/unit/1697/ip:9/il:P

Derived or apomorphic characters have evolved from the ancestral character.
o
o
Synapomorphic characters are derived characters found in two or more species and
suggest a close common ancestor.
http://wordinfo.info/units/view/167/page:3/ip:11
Greek roots:
http://wordinfo.info/units/index/page:11
http://en.wikipedia.org/wiki/List_of_medical_roots,_suffixes_and_prefixes
https://www.msu.edu/~defores1/gre/roots/gre_rts_afx2.htm
Shared derived characters are evidence of evolutionary relationship.
Phylogenetic classification should be monophyletic.
Monophyletic means that all the members of a taxon regardless of rank are descendants of a
common ancestor.
The more recent two species share a common ancestor, the more closely related these two species
are.
A monophyletic group is also called a clade.
Organisms in a polyphyletic group evolved from different ancestors.
Complications in inferring phylogeny
Degree of relationship is based on how recent they share a common ancestor and not on
similarities.
Taxa may be similar because they share ancestral character states or derived character states, but
only the derived character states that are shared among taxa indicate monophyletic groups and
enables us to infer phylogeny successfully.
Character states that are restricted to a single lineage are sometimes called autapomorphies.

Homology: same feature in different species is derived from a common ancestor, e.g. the
forelimb of vertebrates.

Homoplasy: a feature that has evolved two or more times independently of the other and
thus do not have a common origin.

Parallelism: parallelism results in homoplasy; it is an evolutionary process; a similar
feature occurs in different species but their immediate common ancestor was different
and did not have the feature. The similar feature occurs in different but related species,
but it is not present in their immediate common ancestor. They are likely to have similar
evolutionary mechanisms. They are functional adaptations. E.g. Anteater features in
eutheria, metatheria and prototheria.

Convergence: convergence results in homoplasy; is an evolutionary process; two species
with similar phenotype whose common ancestor is very far in the distant past.
Independent genetic origin. The evolutionary mechanisms are different. E.g. the
hydrodynamic morphology of marine predators from the widely separated fish, reptile
and mammalian classes
Some scientists do not consider the distinction between parallelism and convergence meaningful.
Look at the following paragraph that explains the position of eliminating the distinction between
parallel and convergent evolution. This complete article can be found at:
http://people.ibest.uidaho.edu/~bree/courses/19_Arendt_2007.pdf
"Biologists often distinguish 'convergent' from 'parallel' evolution. This distinction usually assumes that when a given
phenotype evolves, the underlying genetic mechanisms are different in distantly related species (convergent) but
similar in closely related species (parallel). However, several examples show that the same phenotype might evolve
among populations within a species by changes in different genes. Conversely, similar phenotypes might evolve in
distantly related species by changes in the same gene. We thus argue that the distinction between 'convergent' and
'parallel' evolution is a false dichotomy, at best representing ends of a continuum. We can simplify our vocabulary; all
instances of the independent evolution of a given phenotype can be described with a single term - convergent." "If the
use of the terms 'parallelism' and 'convergence' cannot be associated with a clear dichotomy, either at a phylogenetic
level or a molecular level, then their continued use is not justified and can even be misleading. They are relics of a time
when we could not evaluate the underlying causes of phenotypic similarity and were confined to inferences based on
comparative anatomy. These terms are also relics of a time when there was not an appreciation of the complexity of
genetic and developmental networks that underlie the determination of simple phenotypic traits, such as coloration. We
argue that this might be a good time to simplify our vocabulary. We need only one term to describe the independent
evolution of phenotypic similarity. 'Convergent evolution' will do nicely."
Jeff Arendt and David Reznick, Convergence and parallelism reconsidered: what have we learned about the genetics of
adaptation? http://people.ibest.uidaho.edu/~bree/courses/19_Arendt_2007.pdf
Parallelism and convergence (homoplasy) can lead to false conclusions about homology.
Evolutionary reversal of a character can also occur.

Evolutionary reversal is the change of an apomorphic character to one similar to an
ancestral character, e.g. dolphins look like fish now, an ancestral character, but they
were terrestrial at one time with the appearance of a terrestrial mammal.
Taxa may be similar because…



They share ancestral character states.
They share derived character states.
They possess homoplasious characters states.
The method of maximum parsimony
Parsimony refers to the principle that states that the simplest explanation requiring the least
number of undocumented assumptions, should be preferred over more complicated hypotheses
that require more assumptions for which evidence is lacking.

The best estimate of true phylogeny requires the fewest number of evolutionary changes.
The ingroup refers to the monophyletic group of species whose phylogeny we want to infer.
The outgroup is made of more distantly related taxa.
Sister groups are groups of species derived from a common ancestor that is not shared with any
other group.
Evaluating phylogenetic hypotheses
The phylogenetic tree obtained from a set of data is a hypothesis that is provisionally accepted.
Additional data may lead to modify or abandon the hypothesis.
The best way to of confirming a phylogenetic hypothesis is to see if it agrees with independent
data, e.g. morphological characters and DNA sequences.

See the example on page 32, Fig. 2.11.
Computer models and experimental populations of bacteria have been used to test the validity of
phylogenetic methods by applying them to phylogenies that are absolutely known.
MOLECULAR CLOCKS
Evolutionary or molecular clock: Some workers assume that mutations are incorporated into the
genome at a fairly regular rate. There is evidence to this effect.

E.g. the shark sequence of the α-hemoglobin chain differs from that of other
vertebrates (human, chicken, carp, salamander) by similar numbers of AA changes.
DNA sequences may evolve and diverge at a constant rate.

Evolutionary differences between organisms arise from mutational differences.

The greater the number of mutational differences, the greater the evolutionary distance
between organisms.
To the extent that the molecular evolutionary clock exists, it can provide a simple way of
estimating phylogeny.
Information from the fossil record on the absolute time of divergence of certain taxa can be used
to calibrate the molecular clock, e.g. the oldest cercopithecoid monkey fossil is dated at 25 My,
providing the minimal estimate time since divergence between the rhesus monkey and the
hominoids. See example on pages 33-34.
Example on page 34:
The formula D = 2rt can be used to estimate the divergence time between two species that have not left a good
fossil record.

D = proportion of base pairs that differ between the two sequences, e.g. 0.0256.




r = the rate of divergence per base pair per My, e.g. 0.001534
t = the time in million years since the species’ common ancestor.
2 represents the two diverging lineages.
t = D/2r or 8.3 My is the best estimate of when the two species diverged from their common ancestor.
The rate of sequence divergence is not necessarily constant.



The rates are quite similar between taxa that are closely related.
Distantly related taxa often have rather different evolutionary rates.
The rate can be used to estimate the absolute age of evolutionary events, such as the
origin of taxa.
GENE TREES
Genes replicate, different copies of a gene, within a single species or more than one species, have
a history of descent from a common ancestral gene just as species do.
The historical relationship among variant DNA sequences of a gene (haplotype) can be used to
construct the phylogeny of a gene, a gene tree.

Haplotype refers to a group of genes that are found in an adjacent place in a chromosome
and are inherited together.
A phylogeny of genes is called a gene tree or gene genealogy.
A DNA sequence is called a haplotype.
When a mutation occurs in an individual, the ancestral haplotype continues to exist in the other
members of the population in which there had been no mutation.
In preparing the gene tree, the sequences that differ the least from each other have the closest
ancestor-descendant relationship; the most closely related haplotypes are connected to each other
by the smallest possible number of mutations.
See example on page 36.
DIFFICULTIES IN PHYLOGENETIC ANALYSIS
1. Evaluating characters is difficult.

Deciding whether or not organisms have the same character state often requires extensive
knowledge of anatomical details and is not an easy or trivial task.

The number of independent characters is difficult to decide. This difficulty also exists at
the molecular level, e.g. rRNA molecule includes short sequences whose bases must pair
to form “stems” so changes in those sequences are not independent; some mammals have
two incisors, a canine, three premolars, and four molars on each side of the haw, while
others do not have teeth, does this represent the loss of one character or four characters?
2. Homoplasy is very common.

It is unwise to rely on particular phylogenetic estimate if other phylogenetic hypotheses
imply just a few extra evolutionary changes.
3. The process of evolution often erases the traces of prior evolutionary history.



If the taxa under study diverged long ago or evolved very rapidly, many of their
characteristics will have diverged so greatly that homologous characters may be difficult
to discern.
In DNA multiple substitutions may occur at a site over the course of time erasing
previous synapomorphies.
If the same substitution occurs in parallel lineages, convergent evolution will occur.
4. Some lineages diverge so rapidly that there is little opportunity for the ancestors of each
monophyletic group to evolve distinctive synapomorphies.

A burst of diversification called adaptive radiation or evolutionary radiation produces
different adaptations in the lineage.
5. An accurately estimated gene tree may imply the wrong species phylogeny.

Some species are polymorphic for the same haplotypes, probably inherited from a
polymorphic common ancestor. These haplotypes do not accurately indicate the
phylogeny of these species.
6. Hybridization. See next section.
HYBRIDIZATION AND HORIZONTAL GENE TRANSFER
Many species of plants and a few species of animals have arisen from hybridization.
Hybridization is the interbreeding of two ancestral species.
Hybridization involves much of the genome.
Evolution by hybridizations is called reticulate evolution. See fig. 2.23, p. 42.
Horizontal or lateral gene transfer usually incorporates just a few genes of one species into the
genome of another species.
This is in contrast of the vertical gene transfer that occurs between parents and offspring.
Lateral gene transfer may occur via a virus, e.g. a group of genes transferred from monkeys to
cats by a viral vector. See lysogenic cycle in bacteria reproduction.
Lateral gene transfer is very important in the evolution of bacteria.
In bacteria genes may be transferred laterally by
 A phage.


Uptake of naked DNA released from dead cells
Conjugation
Phylogenic incongruence and several other lines of evidence have shown that lateral transfer has
provided various bacteria with genes for antibiotic resistance, for the ability to invade hosts and
cause disease, and for adaptations to extreme environments such as hot springs.