Environmental Science · Science

Taxonomy and Phylogeny


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 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 Darwin’s 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, Beta-carotenoids 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.
  • These eukaryotes can move in two paths; path 1: the primitive eukaryote evolved into non-photosynthesis protest, fungal and animal cells. However, path 2: the photosynthesis prokaryote engulfs the primitive eukaryote and become an endosymbiont that evolves into a chloroplast.

Cell and Molecular_

The Origins of Multicellular Organisms

I totally agree with this process. It may give a very clear picture on how ancestral unicellular eukaryotes engulfed photosynthetic bacteria. 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 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. Cretaceous- Tertiary 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. Triassic-Jurassic 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 End-Permian 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.

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.

CaptureErnst 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 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.


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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