PHYLOGENETIC TREE

How to construct phylogeny tree and what they consider
PHYLOGENETIC TREE

      A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities—their phylogeny—based upon similarities and differences in their physical or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor. Phylogenetic trees are central to the field of phylogenetics.
      Or is the branching diagram showing relationship between species bases on their shared common ancestor. A system which is used to organise the diversity of living organism into a phylogeny tree is called systematic. According to Darwin he Cleary considered that the phylogeny tree as an important organizing principle in understanding the concept of evolution, in (Darwin 1859.) He explained the relationship among living groups as a pattern  of branching predates ,  Example of phylogenetic tree.

TYPES OF PHYLOGENIC TREE

Rooted tree
    Is the phylogeny tree which  is directed  with a unique node that corresponding to usually the common ancestor of all the entities at the leaves of the tree. The rooted node do not have parent node but saves the parents of all other nodes in the tree,the root is therefore a node of degree 2 while other internal node have a minimum degree of 3(where degree is the number of incoming or outer coming edges)
   The most common method for rooting tree is the use of an uncontroversial out going –close enough, to allow inference from traits data or molecular sequencing but far enough to be a clear out group. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of the descendants and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematic, and phylogenetic comparative methods.
 Example of rooted tree  see the diagram below




Unrooted tree
 Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry. They do not require the ancestral root to be known or inferred. Unrooted trees can always be generated from rooted ones by simply omitting the root. By contrast, inferring the root of an unrooted tree requires some means of identifying ancestry. This is normally done by including an outgroup in the input data so that the root is necessarily between the outgroup and the rest of the taxa in the tree, or by introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis.

Bifurcating  tree
Both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labelled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a free tree with exactly three neighbour at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbours at some nodes. A labelled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees, more labelled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant; it arises because there are many places on an unrooted tree to put the root. For labelled bifurcating trees, there are:
       
OTHER FORMS OF PHYLOGENETIC TREE
A cladogram is a phylogenetic tree formed using cladistic methods. This type of tree only represents a branching pattern; i.e., its branch spans do not represent time or relative amount of character change

A phylogram is a phylogenetic tree that has branch spans proportional to the amount of character change.

A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch spans.
A spindle diagram (often called a Romerogram after the American palaeontologist Alfred Romer) is the representation of the evolution and abundance of the various taxa through time.

A Dahlgrenogram is a diagram representing a cross section of a phylogenetic tree,

A phylogenetic network is not strictly speaking a tree, but rather a more general graph, or a directed acyclic graph in the case of rooted networks. They are used to overcome some of the limitations inherent to trees.


PHYLOGENY AND CLASSIFICATION
Phylogenetic (cladistic) classification reflects evolutionary history The only objective form of classification – organisms share a true evolutionary history regardless of our arbitrary decisions of how to classify them
ORGANISMS are separated as monophyletic group , paraphyletic group and polyphletic group.

THINGS TO CONSIDER WHEN CONSTRUCTING PHYLOGENIC TREE
On constructing phylogeny tree things that are considered are fossil record, morphological structures embryological pattern of development and chromosomes and macromolecules DNA/ RNA

Fossil record: fossil is the remains of once lived organisms , fossil record often provides clues to evolutionary relationship  that can be used to construct phylogenic tree example by comparing fossils of the past lived organism with the current living organism ,

Morphological pattern : morphology of an organisms provide more information’s which are used to compare   from one organism to another in constructing trees , structures of organisms include both homologous structure and analogous structures example fore limb of horse and fore limb of man there is similar arrangement of bones this indicates that they have the same ancestor and those organisms may be placed at the same branch but regarding with other feature may separate them into different leaves in phylogeny example

Embryological pattern of development : this provide more information on determination of common ancestor of organism required to be put in the beginning of the tree of life because they show great similarity in embryo stages and great different in adult stage

Chromosomes and macromolecules 

Scientist compare macromolecules such as DNA or RNA and protein in different organisms to know the evolutionary that exist for example in the fossils of past lived organisms with current living organisms  and this enable to determine a part where an organism will be organised in the phylogenetic tree.

STEPS TO CONSIDER IN DRAWING PHYLOGENETIC TREE
Selection of model organism for relationship comparison. This consider species breading or nucleotides  (chromosomes and macromolecules) sequence that represents an organism example an organism could be a cow the rest of tree can show how cow is closely related to other organisms based on their genetic traits.
Determination of set of characters : this can be used in comparison between a character and state of an organism and how they are presented in drawing tree of life example organism with four legs  can chew and give live birth or grow hairs . those character can be used to construct tree of life
Divide organisms by considering characters , when an organisms does not contain a desired traits or character , the branch is made in phylogenetic tree to show the difference that exist between two or more organisms of the same ancestor
Continue separating model of organism until each have a single branch in phylogenetic tree  example character  of sheep will separate it from bears and cow onto a singular a singular branch in phylogenic tree

PHYLOGENETIC OR TREE OF LIFE IS IMPORTANT AS FOLLOW

• Understanding and classifying the
• Diversity of life on Earth
• Testing evolutionary hypotheses:

   - trait evolution

   - coevolution

   - mode and pattern of speciation

   - correlated trait evolution

   - biogeography

   - geographic origins

   - age of different taxa

   - nature of molecular evolution

   - disease epidemiology

                                   On construction of phylogeny tree there are some limitations like convergence or parallel evolution example presence of wings in birds and bat and reversals example presence of un ordered characters.
EXAMPLE OF PHYLOGENIC TREE

REFERENCES
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