Midterm 2 Review
Introduction to Phylogeny
Phylogenies can be based on morphological data, physiological data, molecular data or all three.
Today, phylogenies are usually constructed using DNA sequence data. Generally several genes
are used to construct a phylogeny. The genes used may be slowly-evolving (suitable for study
organisms). To construct phylogenies, phylogenetic characters are used – attributes of anf
organism that can provide insights into its history (and shared ancestry). For example,
molecular phylogenies use nucleotide positions as characters, with the character states A, C,
G, or T. Four cladistic character state definitions exist: plesiomorphy, apomorphy,
synapomorphy and autapomorphy. Plesiomorphy refers to the ancestral character state – the
state possessed by the individual at the root of the phylogenetic tree. Apomorphy refers to a
character state that is different from the ancestral state, or derived state. All apomorphies must
be either synapomorphies or autapomorphies. Synapomorphy is a derived character state,
which is shared by two or more taxa, due to inheritance from a common ancestor (these
characters states are phylogenetically informative using the parsimony or cladistic criterion).
Autapomorphy is uniquely derived character state, possessed by only one taxon.
In phylogenies monophyletic groups are groups, which include all of the descendants of a
common ancestor (also known as clades). Synapomorphies identify monophyletic groups. For
example, lactation is a synapomorphy, which identifies mammals as a monophyletic group.
Non-monophyletic groups can be paraphyletic or polyphyletic. Paraphyletic groups are those,
which include some, but not all of the descendants of a common ancestor. For example, with
realization that the group “reptiles” is in fact paraphyletic (did not include birds). As a
consequence birds were included and the resulting monophyletic group was named sauropsida.
Polyphyletic groups are assemblages of taxa that have been erroneously grouped on the basis
of homoplasious characters.
Homology vs. Homoplasy
A character state that is shared between two DNA sequences or taxa may be so because both
inherited it from a common ancestor. In this case the character state would be homologous (a
type of synapomorphy). Alternatively, the shared character state might have evolved in
dependently. In this case it would be a homoplasy. Homoplasy may occur due to parallel
evolution (independent evolution from the same ancestral condition), convergent evolution
(independent evolution from different ancestral conditions) or secondary loss (a reversion to
the ancestral condition). For example, new world vultures (most closely related to storks) and
old world vultures (most closely related to birds of pray) were once erroneously thought to be a
monophyletic group. In fact, they are a polyphyletic group, an example of homoplasy resulting
from convergent evolution. New and old world vultures developed their bald heads separately,
perhaps due to the fact that feathers made their heads difficult to clean. Another example of
convergent evolution is the location and structure of the eye in many species. Analogies
(similarities in function, but not in acquisition of traits) are also examples of homoplasies due to
convergence. An example of parallel evolution is the three spine stickle back. This fish evolved
independently into larger fish and much smaller fish in several lakes. Each morph is more
closely related to the fish from the same lake than from the same morph in another lake.
Positive assortative mating and disruptive selection have played an important role in the
divergence of these pairs.
Mutations may create synapomorphies, while reversals (or back-mutations) may remove them.
Constructing Phylogenetic Trees and Parsimony
Homologous characters (synapomorphies) are used to construct phylogenetic trees and identify
groups that are monophyletic (which is why we say that synapomorphies are phylogenetically
informative). Using homoplasious characters should not be used to construct phylogenies. In
constructing phylogenies, the principle of parsimony needs to be kept in mind. This principle
states that simple explanations are preferred over more complicated ones. In terms of
phylogenetic trees, less evolutionary steps are better than more steps to explain relationships.
The tree with the least number of steps is the most parsimonious. When constructing a
phylogeny for a group of organisms, we need to employ an outgroup, which is not part of the
group of interest (the ingroup), but also not too distantly related to it. The worst mistake we
could make is using an outgroup which is in fact part of the ingroup. The outgroup is used to
polarize the character states, or infer change. The character state possessed by the outgroup is
defined a priori as ancestral (plesiomorphic). We may take whale evolution as an example of the
principle of parsimony.
The artiodactyla is a group of hoofed mammals that possess an even number of toes, and
includes camels, pigs, peccaries, deer, the hippopotamus, cattle and giraffes. The perissodactyla
are hoofed mammals that posses an odd number of toes (e.g. horses, rhinos, tapirs). Two
hypotheses can be formulated to determine whether or not whales belong to the group
artiodactyla: the whales early hypothesis and the whales late hypothesis.
Trait considered Hypothesis Ingroup Outgroup Changes
Morphology Whales early Artiodactyla Perisodactyla 1 – gain
Whales late 2 – gain and loss
Milk protein Whales early Artiodactyla Perisodactyla 47nt
genes Whales late 41nt
Investigating the milk genes to find synapomorphies reveals sites 162, 166 and 177 (see slides,
32 and 33 of Topic 7) as phylogenetically informative. Site 162 identifies the cow, deer, whale
an hippo as a monophyletic group. Site 166 further identifies the hippo and whale as a
monophyletic group. Site 177 identifies the peccary, pig, hippo and whale as a monophyletic
group. This is an example of a homoplasy – site 166 and 177 are in direct conflict. Thus most
parsimonious hypothesis in this case is the wales late hypothesis, because it has less
Aside: Assessing the Confidence in Phylogeny
The bootstrap method is a computational technique for estimating the confidence level of a phylogenetic
hypothesis. It randomly generates new data sets from the original set (1000 replicates is most common)
and computes the number of times that a particular grouping or branch appeared in the tree. For example,
a bootstrap percentage of 100 means that we are 100% confident that the lineages fall under the particular
Phylogeny and Taxonomy
The goal of cladistic taxonomy (cladistics is the use of parsimony to construct evolutionary
relationships) is to only recognize monophyletic groups as valid taxa, but traditional taxonomy
has not always done this. Eukarya (one of the tree domains of life: archaea, bacteria and
eukarya) is taxonomically divided as follows:
Super group Unikonta
The evolution of the amniotic egg (containing the amnion, chorion and allantois – protective
layers) was an important adaptation for life on land and thereby has lead to the partitioning of a
monophyletic group – the amniota. Paraphyletic groups also exist in taxonomy – such ash the
prokaryotes, fish and dicots. Before the whale late hypothesis was accepted the artiodactyla was
also a paraphyletic group. With the addition of the whale a monophyletic group, called
cetartiodactyla was formed.
Biogeography is a branch of science that seeks explanations for why organisms are found in
some regions, but not others. Frequently phylogenies are used to test hypotheses concerning
the geographic origins of different species, or groups of species such as the Chameleons.
Coevolution is the process where evolutionary changes in the traits of one species drive
evolutionary changes in the traits of another species. Coevolution can involve predators and
pray, hosts and parasites, and mutualisms, such as aphids and their endosymbiotic bacteria.
Aphids feed on plant juices, but are not able to digest them. They have a symbiotic relationship
with bacteria in their gut, which digest the juices for them. As a result, there are striking
similarities between the phylogeny of aphids and the bacteria which inhabit their guts
(differences in the phylogenies may arise from wasps laying eggs inside the aphids).
Other Phylogenetic Methods
DNA sequence data allows for powerful methods to be used in phylogenetic reconstruction.
These are collectively referred to as frequency probability methods and include Maximum
Likelihood, and Bayesian methods of phylogenetic inference. These are computationally
intensive and have only been in frequent use for the past 12 years or so, when computers
became powerful enough to accommodate them.
An adaptation is a trait that increases the fitness of an individual relative to individuals that do
not possess the trait. Natural selection is always an adaptive evolutionary force, which can be
aided or hindered by other evolutionary forces, such as genetic drift. The adaptive significance
of some traits is not obvious and testing hypothesis whether traits are adaptive is a major
component of evolutionary biology.
Testing Hypotheses About Adaptation
An example of a hypothesis tested for adaptation is the hypothesis that oxpeckers benefit
mammals by picking the ticks off them and licking open wounds. This hypothesis was tested
using exclusion experiments. Two groups of mammals were segregated. In the first group
oxpeckers were allowed to associate with the mammals. In the second group, oxpeckers were
excluded. This experiment was repeated three times and the change in tick load was measured.
In the oxpecker group, mammal tick load actually increased (though not significantly), while in
the second it decreased slightly. The results were similar for the remaining three trials,
demonstrating that there was no relationship between the presence of oxpeckers and tick count.
Open wounds, however, decreased significantly in the group, which was not exposed to
oxpeckers. The amount of earwax in the mammals not exposed to oxpeckers increased
significantly. This experiment showed that oxpeckers actually feed on mammalian ear wax and
drink blood from open wounds. They are not symbiotes of the mammals, but rather parasites.
This demonstrates the importance of hypothesis testing in biology.
Several important points must be considered when studying adaptations:
1. Differences among populations are not always adaptations
2. Not every trait an organism possesses is adaptive
3. Not every adaptation is perfect
There are three main methods of studying adaptations: experimental studies, observational
studies and comparative studies. Experimental studies are by far the most important method,
because they allow the isolation of a variable and the determination of the effect of a treatment
or situation on that variable. A good experimental design allows the investigation of causation
(does change in one variable cause a response in another?). It is important that correlation is
not confused with causation – many confounding factors may exist and cause correlations, but
not causations. In fact, it is very difficult to say that one variable causes another in biology. An
experiment studied the purpose of the markings on the tephritid fly. The tephritid fly’s primary
predator is the jumping spider, which has markings on its front legs. The spider performs a
territorial threat display by waving its front legs, warning other spiders not to come near.
Tephritid flies wave their marked wings in a way which resembles the jumping spider’s threat
display. Scientists thought that perhaps this is an adaptive trait, which protects the fly from its
predator. However, they were not sure if this would deter other spiders or only jumping spiders
from attacking. To investigate this trait, researchers removed wings from a tephritid fly and
replaced them with those of a regular housefly. They also placed tephritid fly wings on
houseflies and removed and reattached tephritid fly wings to tephritid flies, in order to control
for the wing transplant procedure. What they found was that tephritid flies with marked wings
managed to deter the jumping spider from attacking most of the time, but tephritid flies with
no markings on their wings could not. Other spiders, however, were not deterred by the
markings. Houseflies with tephritid fly wings did not wave their wings and were therefore
attacked by all predators. Thus, this experiment proved that the tephritid fly wing markings
were an adaptive trait, designed to deter the jumping spider from attacking.
An observational study was conducted to determine if garter snakes make an adaptive choice
when they select a nightly retreat. Garter snakes must perform thermoregulation by moving
from a hot to cold environment. During the day they can survive outside (moving from shade
to sun), in burrows (moving deeper in or further out) or under rocks of different thicknesses.
However, at night their selection is more limited – remaining outside (freezing at night), in a
burrow (spending most time outside their preferred temperature range), or in a rock that is too
thick (freezing at night) or too thin (overheating in the morning), is not ideal. The best choice
for snakes at night is a medium sized rock. Researchers determined that most of the time
snakes chose medium rocks for their nightly retreat (adaptive choice).
Comparative studies evaluate the strength of a hypothesis by testing for patterns across
species or lineages. These can include correlations among traits, or among traits as they relate
to environmental features. This type of study requires knowledge of the evolutionary
relationships among the organisms being considered. A comparative study was used to find an
answer to why some bats have larger testes than others. It was hypothesized that this trait is
due to sperm competition (since often female bats will mate with more than one male). If that
were the case, bats living in larger communities would have larger testes (greater competition).
The researches gathered data of different bats living in different group sizes and found a
significant relationship: testes size increased with group size. However, the relationship was
greatly diminished when the inheritance of testes size was examined. When the data was
corrected for relatedness using phylogenetically independent contrasts the relationship was
still present. Another relationship was also discovered: the larger the testes size, the smaller the
Evolution of Adaptive Traits
Four factors limit the evolution of adaptive traits: trade-offs, functional/developmental
constraints, genetic constraints and ecological constraints.
A trade-off is a compromise between one trait and another, which cannot be avoided. An
example of a trade-off in nature is the begonia involucrata flower. B. involucrata has separate male
and female flowers, which are pollenated by bees. Male flower produce nectar, while female
flowers do not. In order to be pollenated, female flowers must mimic the appearance of male
flowers. Intuitively one might think that female flowers would resemble the most rewarding
males with larger flowers (directional selection hypothesis), rather than resemble the average
male flower (stabilizing selection hypothesis). In nature, however, we see that female flower
size is in fact very close to the average male flower size. This is because the larger the female
flower becomes, the fewer flowers can be produced (producing a flower takes energy and
resources). Female flower size is a compromise between the number of flowers grown and
resemblance to the male flower.
A constraint is a factor, which retards the rate of adaptive evolution or prevents a population
from optimizing a trait. An example of a functional (physiological) constraint is the Fuschia
excorticata flower. The F. exorticata flowers contain both male and female parts and are
pollenated by birds. The flowers are initially green flowers produce nectar and attract birds.
After having been pollenated a flower turns red – it no longer contains nectar and birds are not
attracted to it (this ensures efficient pollination). After remaining red for some time the flower
is abscised. Researches endeavored to determine why the expensive red flower is maintained if
it seemingly serves no physiological function. A hypothesis that red flowers serve to
distinguish the plant from surrounding vegetation and attract birds to the green flowers was
tested by removing red flowers and counting bird visits to the plant. It was found that the same
number of birds would visit the plant regardless of the presence or absence of red flowers. Thus
it was determined that a physiological constraint must exist – the flower is red during the time
it takes for the pollen to travel down the stigma in a pollen tube and fertilizes the plant.
Another example of a constraint to adaptation is the Ophraella sp. beetle. This fitofagous beetle
is very closely associated with specific species of plants, having the ability to detoxify their
chemical defenses (so they can reproduce on the host and feed on it). Researchers sought to
determine if all host shifts are possible, or if genetic constraints exist. It was determined that
most species were not capable of contending with the chemical defenses of more than one or
two of the plants tested. Therefore, genetic variation was indeed a constraint. An ecological
constraint is found in species of lice parasitizing different species of doves. Two types of lice
exist: wing-feather lice and body-feather lice. The phylogenies of body-feather lice and doves
are very congruent (an example of parallel evolution), while the phylogenies of wing-feather
lice and doves are not. Wing-feather lice inhabit multiple species of doves, because they are able
to jump onto a type of fly that parasitizes doves and migrate to different species of doves. Body
feather lice are not capable to disperse in this way – they have an ecological constraint (unable
to leave the host).
Aside: Phenotypic Plasticity
Phenotypes arise as a consequence of genotypes and interactions of the genotype with the environment.
Identical genotypes can result in different phenotypes in different environments, which is referred to as
phenotypic plasticity. Several studies have indicated that plasticity itself is an adaptive trait.
Our Closest Relatives
Based on DNA sequence data our closest relatives are those in the monophyletic group
Hominidae and include the orangutan, gorilla, chimpanzee (pan troglodytes) and bonobo (pan
paniscus), the last two being our most immediate relatives. Phylogenetically it has been
determined that the split between the chimp and the bonobo occurred after the spilt between
their common ancestor and the human had already occurred (i.e. humans did not evolve from
chimpanzees). Bonobos are similar to chimps in appearance, but have a less robust body, a
rounder jaw and the hair on their heads is parted in the middle. The bonobo and chimpanzee
are allopatric populations – their distributions do not overlap (they are not found living
together in nature). The two species have radically different behaviour – so different in fact,
that it is impossible to determine what their common ancestor’s behaviour could have been like.
Chimpanzees are aggressive (often hunt other primates for food), while bonobos are much more
docile. Both species live in communities of small groups (fission/fusion societies), but while
small groups of bonobos rarely interact with each other (though they do exchange members