Phylogeny is the history of the evolution of a species or groups, especially in reference to lines of decent and relationships among broad groups of organisms. Fundamental to phylogeny is the preposition, universally accepted in the scientific community that plants or animals of different Species descended from common ancestors. The evidence for such relationships, however, is nearly always incomplete, for the vast majority of species that have ever lived have become extinct, and relatively few of their remains have been preserved (www.MerriamWebster.Com).

Most judgments of phyloganicity, then, are based on indirect evidence and cautions speculation. Even when biologists use the same evidence, they often hypothesize different phylogenies, though they do agree that life is the result of organic descent from earlier ancestors and that true phylogenies are discoverable, at least in principle. Taxonomy, the science of classifying organisms, is based in phylogeny.
Early taxonomic systems had no theoretical basis; organisms were grouped according to apparent similarity. Since the publication of Charles Darwin origin of species in 1859, however, has been based on the accepted prepositions of evolutionary descent and relationship (stanier etal 1987)  
Biologists who postulate a phylogeny derive their most useful evidence from the field of paleontology, comparative anatomy, comparative embryology and biochemistry. Studies of fine structure of cells and geographic distribution of flora and fauna are also useful. The fossil record is often used to determine the phylogeny of groups containing hard body parts; soft parts are generally not preserved.
Most of the data used in making phylogenic judgment have come from comparative anatomy and from embryology. In comparing features common to different species, anatomist try to distinguish between homologies, or similarities inherited from a common ancestors, and, analogies or similarities that arose in response to similar habits and living conditions. Biochemical investigation carried out in the latter half of 20th century has contributed variables data to phylogenetic studies. By counting differences in the sequence of units that make up protein and deoxyribonucleic acid (DNA) molecules, researchers have devised a tool for measuring the degree to which different species have diverged since evolving from a common ancestor.
The earliest organisms were probably the result of a long chemical evolution, in which random reactions in the primeval seas and atmosphere produced amino acids and then proteins.  It is supposed that droplets containing protein then formed membranes by binding Molecules to their surface and these membrane-bound proteins are said to have become organisms when they developed the capacity to reproduce. It is not certain whether   these earliest self-reproducing organisms were proteins, nucleic acid-protein associations, or viruses.
There is general agreement that they were heterotrophic organisms i.e. those that required nourishment in the form of organic matter from early seas. Later, autotrophic forms appeared, having the ability to make their own food from inorganic matter. These organisms were the earliest bacteria; they could store energy as food and release energy as needed through respiration.
Cyanobacteria (sometimes called the blue-green algae) are thought to have been the next evolutionary step in that they were able to use photosynthetic pigments to manufacture their own supply of food and therefore are not totally dependent on their enviroment for nutrition.
After the cyanobacteria there appeared an extensive array of algae; molds, protozoan, plants and animals. Three groups of algae can be dismissed with passing mention, as they arose from uncertain ancestors and have given rise to no further groups. These groups are the Chrysophytes (yellow-green and golden-brown algae, chiefly diatoms); the pyrrophytes (cryptomonands and dinoflagellates); and  rhodophytes, or red algae. Three more group, have greater phylogenetic importance: the chlorophytes (green algae, which almost certainly gave rise to the land plants i.e the bryophytes (mosses and liverworts) and the tracheophytes, or vascular plants (including all of the higher plants); the euglenoids, (unicellular, flagellate organisms), which suggest a broad connection between plants and animals at this primitives level, and the phaeophytes (broken algae), which some biologist have probable source of the animal kingdom. Finally, the protozoans, (unicellular prokaryotic microgarisms) were derives from unknown, more primitive ancestors, and one or more groups of protozoan have given rise to metazoan i.e multicellular animals.
Land plant contains two major groups; Bryophytes and Tracheophytes which differ in many ways but which share distinctive characteristics for adaptation to dry land. These include the housing of the plant embryo in maternal tissue.
Bryophytes are descended from green algae and include mosses, liverworts, and hornworts. Only small quantities of water are needed for their reproduction, so that the sperm may travel to the eggs. The fertilized egg matures within the maternal tissue. The plants is protected from dessication by a waxy cuticle. Bryophytes have apparently not advanced far beyond their algal predecessors and do not seem to be the evolutionary source of other groups.
All the dominant plant on earth are included in the tracheophytes. The tracheophytes development of large plant bodies has been made possible by having vascular parts that carry water and food inside these plants, and by a dominant saprophyte stage with microscopic sized gametophytes. Tracheophytes tissues have differentiated into leaves, stems, and roots, and in the highest plants, seeds and flowers are featured.
In explaining, the evolution of tracheophytes, it has been suggested that a mutant form of green algae developed a primitive rot like function with which to supply itself with water and minerals. The progeny of this organism eventually developed bundles of vascular tissues a stem and leaves and a cuticle for protection. The earlier vascular plants are called psilophytes. The development of seeds arose from the retention of the embryo inside maternal tissues. Early seed ferns gave rise to the gymnosperm group, including pines, spruces, and firs. Flowering plants, the angiosperms, probably came from the gymnosperm phase and have two subgroups. The dicotyledons and the monocotyledons.
The problems of the origin of multicellular animals (metazoans) was long dominated by the German embryologist Ernst Hackle’s theory that the original metazoan ancestor was a spherical protozoa that was structurally similar to the coelentrates (eg. Jellyfishes, corals. Today there are two alternative explanation. The first traces metazoan back to flagellates, the presumed ancestor of flattened, ciliated animals (planulas) that eventually led to coelenterates and flatworms. Another theory hypothesies that multinucleated protzoans, dividing into subcells, were the original metazoans, which developed into simple flatworms. No decisive information, however, yet exist to sustain either contention.
Lower metazoan forms developed the first symmetrical arrangement of body parts about a main axis, thus establishing the bilateral symmetry that characterizes most animals; major exceptions are the echinoderm (eg starfishes, seas cucumbers). The development of tissues into an outer ectoderm, which provides protection and carries sense apparatus, and an inner endoderm, serving digesting and reproduction needs, was an important phase. Another important trend was cephalization (head formation) the anterior end of the body generally holds the central nervous system, sense organs, and mouth.
The current theories postulate the lineage of the higher metazoans. The monophyletic sequence suggest that four  groups evolved from lower forms  to  higher: Ameria (unsegmented animals), which includes flatworms, coelenterates, and mollusks; polymeria (segmented animals), which includes annelids and arthropos.; Oligomeria (reduced segmentation), which includes insects and echinoderms; and chordonia (chordates). (The alternative) diphyletic theory has been proposed by many zoologist. It contends that the higher metazoan had two lines of descent, one of which led to annelids, arthropods and mollusks and the other of which led to echinoderms and chordates.
Humans are included in the chordates. Three basic structures are shared by all chordates: a dorsal nerve tube (brain and spinal cord in vertebrates); a notochord (supporting rod under the nerve tube); and a pharynx perforated by gill slits, at least during the embryonic stage.
The history of evolution is full of examples of primitive groups giving rise to more advanced groups, but it should be noted that it is the more primitives and less specialized members of a group – not the advance member- that produce new groups. For example, birds and mammals arose not form advanced reptiles but from primitive, unspecialized reptiles.
Phylogenetic relationships are illustrated in the form of branched diagrams or trees. A Phylogenic tree is a graph made of branches that connect nodes.


Figure 1. Examples of phylogenetic tree (Prescott et al 1999)

(a)    Unrooted tree joining four taxonomic units
(b)   Rooted tree
The nodes represent taxonomic units such as species or genes; the external nodes, those at the end of the branches, represent living organisms. The length of the branches may represent the number of molecular changes that have taken place between the two nodes. An unrooted tree simply represents phylogenetic relationship but does not provide evolutionary path. The figure1 (a) shows that A is more closely related to C than it is to either B or D, but does not specify the common ancestors for the four species or the direction of change in contrast, the rooted tree (fig 1 (b) ) does give a node that serves as the common ancestors and shows the development of the four species from this root. Pylogenetic tree are developed by comparing molecular sequences. To compare two molecules, their sequences must first be aligned so that similar parts match up. Once the molecule has been aligned, the number of position that varies in the sequences can be determined. These data are used to calculate a measure of the differences between the sequences.Often the difference is expressed as the evolutionary distance. Organisms are than clustered together base on singularity in the sequences. The most similar organisms are clustered together, and then compared with the remaining organism to form a lager cluster associated together at a lower level of similarity or evolutionary distance. The process continue until all organisms are included in the tree.(prescot et al1999) phylogenetic  relationship also can be estimated by techniques such as parsimony analysis             
The data and conclusion of phylogeny show clearly that the world of life is the product of a historical process of evolution and that degrees of resemblance within and between groups correspond to degrees of relationship by descent from common ancestors. A fully developed phylogeny is essential for the devising of a taxonomy that reflects the natural relationship within the world of living things.

Lansing M. Prescott, John P. Harley, Donald A. Klein (1999) General Microbiology Mc Graw – Hill companies, Inc. 4th Edition pg 400, 405-  407 4.
Michael J. Pelczar, JR., E. C. S. Chan, Noel R. krieg.(1999) general   Microbiology Graw – Hill companies, Inc 5th Edition.. pg 314, 324 .
Roger Y. strainer John L. Ingraham mark L . wheels page R. painter .(1987) General microbiology, macmiikan press LTD hound mils, basingstoka, hampshare 5th edition .pg 895
WWW. UCMP . Berkeley edu/ exhibid/phylogeny
(WWW. Merriam – Wlebster. Com /../ Phylogeny)
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