Phylogenetic trees depict the evolutionary relationships among species and other taxa. They branch to show how taxa are related through inferred common ancestors. Charles Darwin popularized the concept of an evolutionary "tree" in his 1859 book On the Origin of Species. Today, phylogenetic trees effectively convey how speciation occurs through the splitting of lineages over time. Various types of phylogenetic trees exist, including rooted trees that show ancestry and unrooted trees that simply illustrate relatedness among taxa. Computational methods are used to build phylogenetic trees from genetic and genomic data, though trees have limitations and may not fully represent the evolutionary histories of included taxa.

1. PHYLOGENY & EVOLUTION

2. 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.

3. The 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.

4. 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.

5. 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.

6. Special tree types[edit]
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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.

7. 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).

8. 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?)

9. Although 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.

10. 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

11. NAME: RAZIA MAHRAM
ROLL NO. 3035
CLASS: BS(H) BOTANY 3rd SEMESTER(EVNING)
UNIVESITY OF EDUCATION OKARA