TOPIC

PHYLOGENY & EVOLUTION

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.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.

PHYLOGENETIC TREE

HISTORYThe idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower to higher forms of life (such as in the Great Chain of Being). Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the notion of an evolutionary "tree" in his seminal book The Origin of Species. Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and semirandom splitting of lineages. Over time, species classification has become less static and more dynamic.

Rooted tree A phylogenetic tree, showing how Eukaryota

and Archaea are more closely related to each other than to Bacteria, based on Cavalier-Smith's theory of bacterial evolution. (Cf. LUCA, Neomura.)

A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup—close enough to allow inference from sequence or trait data, but far enough to be a clear outgroup.

TYPES

A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection. Meanwhile, low genetic diversity (see inbreeding and population bottlenecks) can caus 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.[2] 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.

UNROOTED TREE

SPECIAL TREE TYPES

Special tree types[edit] This section does not cite any references or sources. Please help

improve this section by adding citations to reliable sources. Unsourced material may be challenged and removed. (October 2012)

Fig. 3: A spindle diagram, showing the evolution of the vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are often used in evolutionary taxonomy.

Fig. 4: A highly resolved, automatically generated tree of life, based on completely sequenced genomes.[5][6]

A dendrogram is a broad term for the diagrammatic representation of a 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.

3. Tertiary gene pool (GP-3): Members of this gene pool are more distantly related to the members of the primary gene pool. The primary and tertiary gene pools can be intermated, but gene transfer between them is impossible without the use of "rather extreme or radical measures" [1] such as:◦ embryo rescue (or embryo culture, a form of plant

organ culture)◦ induced polyploidy (chromosome doubling)◦ bridging crosses (e.g., with members of the secondary

gene pool).

Gene pool concept in crop breeding

Main article: Computational phylogenetics Phylogenetic trees among a nontrivial number of input sequences are

constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which calculate genetic distance from multiple sequence alignments, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as ClustalW also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction. Maximum parsimony is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the optimality criterion of maximum likelihood, often within a Bayesian Framework, and apply an explicit model of evolution to phylogenetic tree estimation.[4] Identifying the optimal tree using many of these techniques is NP-hard,[4] so heuristic search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data.

Tree-building methods can be assessed on the basis of several criteria:[7]

efficiency (how long does it take to compute the answer, how much memory does it need?)

power (does it make good use of the data, or is information being wasted?)

CONSTRUCTION

LIMITATIONSAlthough phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, they have important limitations. They do not necessarily accurately represent the evolutionary history of the included taxa. The data on which they are based is noisy; the analysis can be confounded by genetic recombination,[9] horizontal gene transfer,[10] hybridisation between species that were not nearest neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences.

The "tree of life Evolutionary history of life, an overview of

the major time periods of life on earth Life, the top level for Wikipedia articles on

living species, reflecting a diversity of classification systems.

Three-domain system (cell types) Wikispecies, an external Wikimedia

Foundation project to construct a "tree of life" appropriate for use by scientists

SEE ALSO

STUDENT INFORMATION

NAME: RAZIA MAHRAM ROLL NO.3035 CLASS: BS(H) BOTANY 3rd

SEMESTER(EVNING)

UNIVESITY OF EDUCATION OKARA

END