● How did you decide which characters to use for the phylogeny?

y? How did you decide which character

states were primitive and which were derived?
All characters were eventually used in the phylogeny. However, in order to determine which
characters to prioritize or which would largely influence the formation of the final cladogram, we used
the character matrix in identifying the character states which certain species had in common. Once
we saw patterns where groups of species shared the same character states, we were able to conclude
that these characters were to be prioritized in the phylogeny or that these characters largely influenced
the categorization/grouping of the given species. An example of this process at work was when we
saw how only the gold and silver dragons had human forms. With this, human form was an apomorphy
specific to the gold and silver dragons and as such, was an important character to consider in grouping
the draconic species.
In deciding which character states were primitive, we started by identifying the “odd one out,” that is
which character state appeared in only one species. For example, upon seeing that ‘a tail ending in
stinger ‘, ’four limbs’, and ‘incapable of speech’ were expressed in only one species, we were able to
say that these three states were primitive. We then used these states as the basis for determining
which states from the remaining characters were primitive and which were derived. For example, the
wyvern possessed the primitive state of having only four limbs. Since the wyvern had chromatic scales
and did not have a breath weapon or a human form, we deduced that these three states were
primitive.

● What is your outgroup? Why does it make sense that it is the outgroup?
The outgroup of our cladogram is the wyvern. While it shares several characteristics with the other
draconic species (i.e. limbs modified into wings, scales, and tail), it is the only species with four limbs
and no breath weapon. It is also the only species with a tail stinger, as compared to the other draconic
species who possessed normal tails. This particular character state is likely an apomorphy
(autapomorphy) specific to the wyvern. Having said these, it makes sense that that wyvern is the
outgroup, a species closely related to the other species but is not included within a taxon.
(https://www.biology-online.org/dictionary/Outgroup)

● Are there any homoplasies among the draconic species? What are they?
There are homoplasies (i.e. independent origins of the same character state in different lineages)
among the draconic species, namely: the fire breath weapon and the ice breath weapon. The fire
breath weapon appeared in both the red dragon and the gold dragon. This weapon emerged
independently in these two draconic species. Similarly, the ice breath weapon came about
independently in the white dragon and the silver dragon.

1. Is your cladogram parsimonious? Justify your answer.

Our cladogram is parsimonious. This is because only two homoplasies were identified. This is a very
small number of incidences when the same character state emerged independently in different
lineages. There are significantly more synapomorphies and autapomorphies present in the
cladogram which show that most of the character states of the draconic species were present in the
shared ancestors of the taxa determined and that these states did not merely appear independently
in species from different lineages. These indicate that the draconic species were grouped into taxa
correctly following the principle of maximum parsimony.

1. Is having two breath weapons an adaptation? Justify your answer.

An adaptation is a feature that allows an organism to be better fitted to survive and multiply in its
environment. Having said this, we can conclude that having two breath weapons is an adaptation
because it would grant a dragon a competitive advantage over other species that possess either only
one or no breath weapon. A dragon with two breath weapons can use two different elements, instead
of none or just one, to better defend itself against other dragons/predatory species and to better catch
prey as well. Since such dragons would be less likely to die because of competition or lack of nutrition,
having two breath weapons indeed increased the species’ fitness and as such, is an adaptation.
1. Why are fictional organisms like dragons useful tools in exercises such as this? What are their
limitations as such?
Fictional organisms such as dragons tend to pique students’ interest which makes studying biological
concepts such as taxonomy and systematics using such tools appealing and entertaining to us
learners. Using fictional organisms also helps us visualize important concepts in systematics, such
as evolutionary relationships, hierarchical classification, and parsimony. It is an effective way of
testing our mastery on the biological concepts we learned in class since we are able to apply them to
hypothetical creatures. Similarly, this method challenges us to think critically and to solve problems
efficiently. Lastly, in this particular exercise on draconic species, the given character states are simple
and distinct which makes the evolutionary relationships between the species clear and evident.
Despite the undeniable benefits of using fictional organisms in the study of systematics, the method
still has its share of limitations. Since these hypothetical creatures have hypothetical characteristics
which do not necessarily appear in real life or fit into any existing taxa, using such creatures in
practicing systematics does not fully simulate how it is to classify and categorize actual living
organisms. Furthermore, the method may not always clearly depict the principles that govern
evolution (e.g. gradualism, populational selection, etc.). As such, using fictional organisms to simplify
systematics may be counterproductive given that evolution is far more complex than this method
paints it to be.

1. How would you modify this exercise to illustrate some of the common concepts of Darwinian
evolution?
This exercise, as is, already illustrates common descent or descent with modification. However, in
this exercise, the environmental conditions experienced by the draconic species were not given,
hence it was difficult to determine what factors contributed to the emergence and selection of certain
adaptations or character states in general. As such, natural selection and populational selection, two
important concepts in Darwinian evolution, were not easily observable in this exercise. This issue
could be addressed by providing some context into the background conditions/ecological pressures
the draconic species were exposed to. This modification would shed light as to why certain character
states became adaptations that increased fitness leading to them persisting and being inherited by
the less primitive dragon species.

1. In a cladogram of all animals, what would be a good outgroup?

A good outgroup for a cladogram of all animals would be class Choanoflagellatea. Choanoflagellates,
which comprise this group, are small single-celled aquatic protists who take their name (“collar-
flagellates”) from the closely packed microvilli that surround their single flagellum.
(http://www.ucmp.berkeley.edu/protista/choanos.html). These protists are considered as the closest
predecessor of animals (metazoans) as evidenced by their very close physical similarities to the filter-
feeding cells or choanocytes of sponges. Sponges from the animal phylum Porifera are among the
most primitive animals, hence it can be concluded that choanoflagellates and animals are closely
related
(http://cfb.unh.edu/phycokey/Choices/Amoebae_Flagellates_Ciliates/Choanoflagellates/choanoflage
llates_key.html). However, since choanoflagellates are unicellular protists while animals are
multicellular metazoans, choanoflagellates cannot be included in the taxon of kingdom Animalia,
thereby making them the outgroup.

1. Based on your research, are there phyla whose phylogenetic place is problematic? Which ones and
how so?
1. How can databases like the Catalogue of Life be useful in the study of animal diversity?
Animals are among the most complex organisms on earth. With respect to this, the animal kingdom
as a whole exhibits extraordinary diversity and complexity, as well. Time and again, scientists face
the perennial problem of organizing the species under kingdom Animalia into one, unified, coherent,
and parsimonious phylogenetic tree while at the same taking into consideration their complex and
various characteristics. Databases such as the Catalogue of Life are useful as they are clear records
of the prevailing/most updated biological classification of living organisms, as formed by scientists.
Scientists then continually build upon these existing records as they gain new knowledge on animal
diversity. Furthermore, these databases judiciously compile and regularly update the large wealth of
data and research on biodiversity and present it in a digestible form. This makes it easier for scientists
and lay people alike to learn about, understand, and be updated on their taxon/taxa of interest.
Moreover, these databases can be used in determining similarities and differences between taxa
which allows people to better grasp how diverse animals are. Lastly, databases such as the Catalogue
of Life allow us to assess the “health” of animal taxa (whether they are slowly becoming endangered,
have become extinct, etc.). As a result, these databases contribute to animal diversity conservation
efforts by monitoring species and spreading awareness on them through information dissemination.

1. What insights on diversity of animal life on Earth can one glean from the database?
Animal life on Earth is indeed diverse. While it seems that there are already so many known species
of animals, the database tells us that there are actually so many animal species we have yet to
discover, name, and catalogue. This fact sheds light on how ubiquitous and massive kingdom
Animalia truly is. It is very much a possibility that once more species are catalogued, the existing
taxonomic classifications, and consequently the database itself, would drastically change. Sadly, the
database also tells us how many species (58,864 to be specific) are already extinct. While many of
these species slowly went extinct due to natural causes, it cannot be denied that humans are the
primary reason why thousands of species are being wiped out within such a short amount of time. To
illustrate how drastic human-caused extinction is, extinction, a natural phenomenon, occurs at a
natural “background” rate of approximately one to five species per year. Scientists estimate that
species are going extinct now at 1,000 to 10,000 times this background rate. In the last 500 years
alone, 1,000 species were recorded to have gone extinct.
(https://www.biologicaldiversity.org/programs/biodiversity/elements_of_biodiversity/extinction_crisis/
) This is a tremendous loss in biodiversity within such an extremely short amount of time when viewed
in the context of the geologic time scale. Having said all these, the database makes us realize that
we must do our best as a species to record and catalogue as many animal species as we can and to
do even more to protect them from endangerment and extinction.

1. What research problems can be addressed with data from this database?
The following research problems can be addressed using data from the Catalogue of Life database:
● What major characters determine taxa
● which phyla are exhibiting concerning extinction rates