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TAXONOMY AND PHYLOGENY

ANIMAL CLASSIFICATION

Abstract
During the history of science, many biologists tried to name and describe animal
species. There are several theories and hypothesis to classify and name species. It is
vital to understand the role and goal of taxonomy related to the evolution of animals
and how taxonomy impacts the science of evolution. More studies have been taken
on unicellular organisms and their processes. One of the crucial processes is
symbiogenesis. Biologists studied the process of symbiogenesis and they linked it to
the increasing amount of oxygen in early ages. They found several strategies on how
organisms adapted to this great oxidation event. Scientists argued that some events
caused a mass distinction of species at different ages. They also discussed how these
losses affect the classification of species. Another new factors can influence the
biodiversity of species, such as human factors and environmental factors.
DOI: 10.13140/RG.2.1.3336.6169

SAMEH F. ABDELGHANY

TAXONOMY AND PHYLOGENY

Taxonomy and Phylogeny


Introduction
During the history of science, many biologists tried to name and describe animal species. There are
several theories and hypothesis to classify and name species. It is vital to understand the role and
goal of taxonomy related to the evolution of animals and how taxonomy impacts the science of
evolution. More studies have been taken on unicellular organisms and their processes. One of the
crucial processes is symbiogenesis. Biologists studied the process of symbiogenesis and they linked
it to the increasing amount of oxygen in early ages. They found several strategies on how organisms
adapted to this great oxidation event. Scientists argued that some events caused a mass distinction
of species at different ages. They also discussed how these losses affect the classification of species.
Another new factors can influence the biodiversity of species, such as human factors and
environmental factors.
Taxonomy and Animal Grouping
Scientists tried to grouping and classify animal in different ways. They attempted to classify, the name
of animals in the traditional taxonomy. They also attempted to show the relationships by descent and
indicate the degree of resemble. They failed to fulfill all of these features as they wanted to implement
all at the same time. Aristotle invented the early form of classification. His classification based on all
living organisms in his time as animals and plants. He also attempted to classify animals based on the
methods of their transportation (Biodiversity-worldwide.info, 2016). Modern biologists used some
methods to classify traits of both anatomical and homologous structures. They used body symmetry
- bilateral, radical or asymmetrical, type of body skeleton exoskeleton, or endoskeleton,
segmentation, body covering and the presence of body appendages. (Jarrell, 3003). Personally, I do
not think that these methods of classification are accurate. I believe that Cladistics Analysis,
evolutionary systematic and phonetics methods are most accurate. Cladistics Analysis is the most
widely used in the taxonomy. It is used to classify traits in order to match their evolutionary history.
Evolutionary Systematics is by the observation of the degree of evolutionary characteristics of the
organism. Phonetics classification is similar to the evolutionary systematic, but it does not attempt
to build any evolutionary linkages (Infoplease.com, 2016).
Taxonomy is imperative to describe the diversity of the living world and to understand its processes.
It is also used to identify, naming, describe living organisms. I believe that taxonomy is vital in many
fields of science. In paleontology, if we do not have a good system for taxonomy, we would not be
able to understand the old life and its processes. Furthermore, we would not be able to classify and
dating different rocks in geology. Taxonomy is also necessary for the modern science. It might help
in the genetic draft and modification of the organisms; it is also crucial for conservation of the
biodiversity (Cain, 2014). It also helps us to explain the relationships between different species.
It is true that the classification of animal is very related to the evolution. The old classification is based
on the morphological characters of the trait while the modern classification shows the evolutionary
relationships among species. I think the most important thing is that most biologists agreed to group
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animals according to shared evolutionary history. In this case, the grouping results in an organized
classification that contain information regarding our standing in the evolutionary history of these
groups. Natural classification groups together feature of animals that are seen to be related. I would
maintain that natural classification is important in providing a concision and valuable information of
the grouping of animals.
Process of Symbiogenesis
Symbiogenesis is the symbiotic merger of two different organisms to produce a third new one
(Shapiro, 2012). It is called Endosymbiotic Theory. To explain this process, I will need to mention the
example of the successful of a eukaryotic cell is the symbiogenesis between two prokaryotes
organelles- mitochondrion and the chloroplast. The mitochondrion obtains energy from glucose by
consuming oxygen to produce carbon dioxide and water. The chloroplast consumes the product of
mitochondrion. It also receives energy from light converting it into chemical energy of glucose and
producing oxygen (Gilman, Peterson, and Mikulecky, 2008). I believe this relationship between two
organelles is a win-a-win relationship, but I argue that one organelle might become a willing prisoner
to a delightful host. The prisoner might have to provide a diet to the warden. The prisoner, in turn,
would have received the protection of the harsh outer environment. I would like to maintain that this
relationship might help in the evolution of these prokaryotic organelles.
There are some evolutionary strategies that anaerobic organisms coped with increasing amounts of
oxygen in the early atmosphere. Billion years ago, dioxygen that is biologically produced, started to
accumulate in small areas, or layers of cyanobacterial photosynthesize mats. These cyanobacteria
have been developed to deal partially with the dioxygen. Primitive anaerobes adapted to these
changes in different ways. The easiest way is to avoid dioxygen. An evidence of this method is the
deep ocean remained anoxic for an extended period even after the dioxygen started to accumulate in
surface layers. I personally support this theory. The second strategy is the anaerobes have the ability
to hide and gain some time to evolve defenses. I partially disagree with this approach as I cannot find
any evidence for this strategy. However, it might be reasonable if we considered Darwins theory of
Natural Selection. The third approach, which I totally agree with it, antioxidants systems might have
evolved. Some of these systems exist in all life forms. There are two kinds of antioxidants- small
molecules that remove oxygen (Scavenger) by reacting with Reactive Oxygen Species (ROS), (Ray,
Huang, and Tsuji, 2012), and enzyme system that detoxifies them (Decker & Holde, 2011). Some
examples of scavenger molecules are; Ascorbic Acid, Alpha-Tocopherol or vitamin E, Betacarotenoids and Resveratrol. There are also some defenses strategies that are evolved. These
strategies are, aggregation to avoid ROS, formation of melanin, and prevent creation of oxygen
radicals by oxygen transport proteins
Endosymbiosis of Anaerobic Organisms, (Karp, 2010).
-

Step 1: a small aerobic prokaryote engulfed in the vast anaerobic prokaryote.


Step 2: a mitochondrion evolved from the aerobic endosymbiont.
Step 3: the protein of the plasma membrane has to evolve into a nuclear envelope. In this step,
the primitive eukaryotes created and produce two major groups of eukaryotes.
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These eukaryotes can move in two paths; path 1: the primitive eukaryote evolved into nonphotosynthesis protest, fungal and animal cells. However, path 2: the photosynthesis
prokaryote engulfs the primitive eukaryote and become an endosymbiont that evolves into a
chloroplast.

Karp, G. (2010). Cell and molecular biology. Hoboken, NJ: John Wiley.

I totally agree with this process. It may give a very clear picture on how ancestral unicellular
eukaryotes engulfed photosynthetic bacteria.
The Origins of Multicellular Organisms
There are three basic theories for the physical mechanism of the origin of multicellular organisms,
symbiosis, coenocytial and colonial, (Letton, 2016). Symbiosis Theory, which are cells of different
unicellular species, gain common benefits from aggregation and evolve to be a multicellular
organism. This hypothesis has some pros. It needs to invoke kin selection to prevent nutrition
competition, and the two organelles provide the required nutrition that both are needed. This
hypothesis, I guess, cannot offer any explicit mechanism in how two separate genomes can have fused
into a single genome. In the case of mitochondria and chloroplasts, these organelles still have
different genomes. This process might take hundreds of millions of years to be multicellular. This is
a problem of this theory as it has many cons rather than pros. From my point of view, I can see that
this theory is very weak to explain the origin of multicellular organisms. Coenocytial Theory, the
evolution of multiple nuclei single cell by partition. Each nucleus will be separated by a membrane
creating a multicellular organism. This is an excellent and acceptable theory as the cell with has some
multiple nuclei can be partitioned into multicellular organisms, for example, the intermodal cells of
the algae Chara and many filamentous fungi. Another good example is seen in the Fruit fly Drosophila
in the embryonic development. Many cells are formed from coenocytia. I think the only issue in this
theory is that it needs complex single cells which have multiple nuclei. Colonial Theory, it
considered the most acceptable method. Its mechanism is that the single cell divides to form two
daughter cells. These two daughter cells fail to separate and fuse together to produce a colony of
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fused or attached cells. It is also produced by selective pressures that lead to segregation of somatic
cells and germ that aggregate to form a colony. There are several examples of colonial organisms
such as choanoflagellates from spherical colonies. The colonies that result from failure to separate
show high levels of relatedness rather than results from aggregation. Personally, I cannot find any
issues in this theory. I prefer to believe this theory rather than another two theories.
Many opinions support the colonial theory. The evidence can be extracted from similarities in some
complicated biochemical path and RNA sequences. Choanoflagellates look similar to the feeding
system of sponges. They also have the same number of genes. Another opinion can be seen in the
example of Tyrosine Kinases (TK) enzymes. It was identified in the choanoflagellates in the early ages
of metazoans. It was believed that choanoflagellates have more TK genes than any animal and many
components of the TK signaling pathway as well (Akst, 2011). Some scientists have an evidence of
the development of multicellular, which I completely agree, in the choanoflagellates homologs if
cadherin. This is the cell-cell adhesion and signaling in animals. This evidence proved that
choanoflagellates are said to be the common ancestor of animal and fungi.
Different Losses of Species Species Extinctions
During the history of the life on earth, there were five mass extinctions that vast numbers of animal
and plant groups are disappeared. More than 90% of all organisms are extinct, (National Geographic,
2016). The mass extinction periods are; Cretaceous Extinction, Triassic-Jurassic Extinction, The
Permian-Triassic Extinction, Devonian Extinction, and Ordovician Silurian Extinction. CretaceousTertiary mass extinction occurred 65 million years ago (bbc.co.uk, 2016). This mass extinction
period is famed for the loss of dinosaurs. Another organism extinct at this time such as ammonites,
and many flowering plants. As a result of flood basalt eruptions, the world climate affected and some
of the severe falls in sea level were the main reasons for this extinction. I believe the primary cause
of this extinction might be the emission of toxic gases such as H2S or Methane gases. TriassicJurassic extinction is called End-Triassic extinction. It is occurred at the end of Triassic period, 252
million to 201 million years ago that result in extinct of 20% of all taxonomic families and 76% of all
marine and terrestrial species, (Encyclopedia Britannica, 2016). I think that this mass extinction
helped dinosaurs to become dominant animal on Earth. Permian Mass Extinction, is also called EndPermian Mass Extinction. It is occurred about 252.3 million years ago, killing about 96% of marine
life and 70% of terrestrial life (Sci-news.com, 2014). From the figures, I believe that it is one of the
most severe mass extinction. The late Devonian Extinction, around 75% of the species and 50% of
the genera in the marine are dead (Elewa, 2008). Ordovician- Silurian Extinction, occurred 443
million years ago, was the first event of mass extinction during earth history. About 57% of genera
and 255 of families extinct (Hallam and Wignall, 1997). These losses affected the classification of
some species as there were some missing links between species in their evolutionary tree. This also
affects the long-term evolutionary pattern of species diversification. I agree with this idea, as some
fossils showed that the mass extinction not only removed the evolution lineage, but they affected by
long-term influence on the evolutionary rate. This can be seen in the fossils of Mollusks in Maryland,
USA.

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From the previous overview of species losses, I can argue here that without the science of taxonomy,
we would not be able to identify families and organisms that were existed and gone. It also can give
us a chance to explore the geological history as I believe that there are several organisms are missing
in the modern and old taxonomy.
New Species Classification
Carl Linnaeus, 1758, (Bio.slu.edu, 2016), established a classification system as he divided plants and
animals into Kingdom, class, order, genus, species and variety. However, he also creates a binomial
nomenclature. It consists of a genus and species name. The genetic names are in Latin and always
begin with capital letters while species name always begin with lower-case letters, for example, Homo
Sapiens. This is a magnificent method of nomenclature, I believe. It can give a clear identification to
species. However, there are some other methods to classify the species. Some taxonomists added the
author name- who first officially describe the present case, for example, Rhinacloa pallips, Reuter.
Some scientists believe that it is confusing, especially for public and non-scientific people. I partially
agree. However, it is crucial if some species have too close spellings. From the previous example,
there are Rhinacloa pallips, Reuter, and Rhinacloa pallidipes, Maldonado. Some scientists added some
sub-groups to the Linnaeus classification. They added subclass, infraclass underclass category and
suborder under order category. I think this is an inappropriate way to classify a species. It will give a
long name that would be hard to remember.

Bio.slu.edu. (2016). Nomenclature, Classification. [online] Available at: http://bio.slu.edu/mayden/systematics/bsc420520lect2.html


[Accessed 11 Mar. 2016].

Ernst Mayr, 1942, (Mayr, 1999), identified that the subspecies level was far from the perfect solution.
Subspecies were not, sometimes, distinct from each other. Mayr discovered new species of birds and
sketching their ranges. He discussed some species concepts such as; static and strictly morphological
species concepts of Linnaeus that are based on appearance differences, Practical species concept, that
is based on competent systematics, the genetic species concept, that is based on the genetics. The
concept that is based on the interfertility is sterility species concept, and biological species
identification (Chung, 2003). I totally agree with what Mayr argued. He tried to explain the change
from morphological species concept to biological species concept. The problem is that after Mayr
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interpretation of the classification based on the species population, some taxonomists try to invent
trinomial names. This method of the classification, I guess, is too long to be known and it might make
a confusion between the new and old systematics.
Challenges Within Species
Many factors affect the diversity of a species. Many species are threatened due to some critical
factors, such as human activities, and environmental change or damaged.
Human Factors:
Human plays a vital role in threatening species diversity. Some of the activities that are threatening
species. Overfishing: is the greatest threat to the marine biodiversity. As a result of this action, some
tuna species are threatening. Urbanization: as the human intend to build new cities and towns. This
will destroy the biodiversity of some animals leading to losing the nutrition and destroy the suitable
living environment to these animals. Overhunting: some people hunt animals for sports, food,
fashion, and keep them as pets, for example, human hunt tigers for fashion. Growing of human
population: will threat the diet of some species. The destruction of habits through agriculture.
Industrial activities that released toxins and wastes in a wild area. These impact the animal
population as some chemicals might affect the fertility of an animal.
Environmental Factors:
Global warming: as a result of human activities that help increase emission of Carbon-containing
substances, the weather of the earth is changing. This change may lead some animals to travel to
another area. The animals will be threatening if they could not adapt to the new environment. Air,
water and soil pollution. The environmental degradation has an enormous impact on the species
survival. Overpopulation can help to increase the degradation of an environment. Ozone depletion
is the second most impact that can affect species survival. It helps in increase the earth temperature.
The penetration of ultraviolet radiation affects all kind of organisms. In human, for example, it can
contribute to increasing cancer diseases.
Conclusion
Many scientists have established several classification strategies. Some of them are useful and valid
others are not. The old method of classification invented by Aristotle is an initial attempt to classify
species. However, modern methods provided an excellent system of classification. This gave a
significant understanding of the role of taxonomy in different fields such as identifying and naming
of species and in the genetic draft and modification as well. The process of symbiogenesis helped to
understand the process by which ancestral unicellular eukaryotes engulfed photosynthetic bacteria.
It also supports the idea of from where multicellular animals come. Finally, the five mass extinction
events affected the evolutionary lineage of species and made a considerable debate among biologists
about the missing links in the evolutionary tree of species.

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SAMEH F. ABDELGHANY

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