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Exercise 8: Morphological Examination Exercise 11: Phylogenetic Tree Construction: Single Marker Analysis

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Kamille Poblete

This document describes techniques for morphological examination and phylogenetic tree construction using single marker analysis. It discusses examining the external and internal morphology and diagnostic features of organisms. It also explains that phylogenetic tree diagrams depict the genealogical relationships of organisms based on analyses using bioinformatics and phylogenetic software. The document outlines different phylogenetic analysis methods including maximum parsimony, maximum likelihood, and Bayesian inference and describes how they infer relationships based on evolutionary models and gene sequence data. It also lists several popular phylogenetic software tools used to conduct these analyses and construct organismal phylogenetic trees.

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Exercise 8: Morphological Examination Exercise 11: Phylogenetic Tree Construction: Single Marker Analysis

Uploaded by

Kamille Poblete
35 views2 pages
This document describes techniques for morphological examination and phylogenetic tree construction using single marker analysis. It discusses examining the external and internal morphology and diagnostic features of organisms. It also explains that phylogenetic tree diagrams depict the genealogical relationships of organisms based on analyses using bioinformatics and phylogenetic software. The document outlines different phylogenetic analysis methods including maximum parsimony, maximum likelihood, and Bayesian inference and describes how they infer relationships based on evolutionary models and gene sequence data. It also lists several popular phylogenetic software tools used to conduct these analyses and construct organismal phylogenetic trees.

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EX-8-11-REVIEWER

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This document describes techniques for morphological examination and phylogenetic tree construction using single marker analysis. It discusses examining the external and internal morphology and diagnostic features of organisms. It also explains that phylogenetic tree diagrams depict the genealogical relationships of organisms based on analyses using bioinformatics and phylogenetic software. The document outlines different phylogenetic analysis methods including maximum parsimony, maximum likelihood, and Bayesian inference and describes how they infer relationships based on evolutionary models and gene sequence data. It also lists several popular phylogenetic software tools used to conduct these analyses and construct organismal phylogenetic trees.

Copyright:

© All Rights Reserved
Download as PDF, TXT or read online from Scribd
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35 views2 pages

Exercise 8: Morphological Examination Exercise 11: Phylogenetic Tree Construction: Single Marker Analysis

Uploaded by

Kamille Poblete
This document describes techniques for morphological examination and phylogenetic tree construction using single marker analysis. It discusses examining the external and internal morphology and diagnostic features of organisms. It also explains that phylogenetic tree diagrams depict the genealogical relationships of organisms based on analyses using bioinformatics and phylogenetic software. The document outlines different phylogenetic analysis methods including maximum parsimony, maximum likelihood, and Bayesian inference and describes how they infer relationships based on evolutionary models and gene sequence data. It also lists several popular phylogenetic software tools used to conduct these analyses and construct organismal phylogenetic trees.

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SYSTEMATICS LAB

Exercise 8: Morphological Examination Exercise 11: Phylogenetic Tree Construction:


Single Marker Analysis
o Morphology: is defined as the form and
structure of biological organism along with o To determine the relationship of the target
their specific characteristics and features. taxa, bioinformatics and phylogenetic
(shape, structure, size, color, etc.) softwares are employed.
o Internal morphology (aka anatomy): o Tree diagrams:
involves detailed examination of the internal  Result of these analyses, topology of
structures from organ systems, organs, tissues the investigated samples
and cells.  Tree graphs that depict the
o Diagnostic features: are sets of important genealogical relationships of
characters that separate a taxon from other organisms.
similar or closely related taxa, just like  Shows relationships: dichotomy and
Panthera tigris (tiger) being easily polytomy
distinguished by its stripes when compared o Polytomy
to Panthera leo (lion).  As seen in a bracketed cladogram
o Phenotypic variations: within a population  Results from missing data analysis
belonging to the same species, subtle
differences in morphology are observed. Phylogenetic Analysis
(ex: variation within human population are 1. Maximum Parsimony (MP) Analysis
in the form of height, weight, body shape,  Based on principle of parsimony,
skin color, etc.) evolution of any particular set of
o Phenotypic plasticity: is also known as the characters using the smallest number
reaction of as species to an unfavorable of evolutionary changes of the
condition, thus will respond by a shift in analyzed characters
behavior or physiology, or change in  Trees of the minimum length (least
morphology in order to adapt to the number of steps) are considered the
habitat. Impacts on diversification and most parsimonious
speciation.  Bootstrap support (BS) values:
o Species description: must bear a complete  Numbers found on nodes
and comprehensive enumeration of  Ranges 0-100%
characters and its different states, and must  Provide reliability of the
include a diagnosis. analysis
o Diagnosis: distinguishing characters  Relates how “good” was the
EXAMPLE: investigated phylogenetic
data
 Two test homoplasy: reliability for both
must be closer to 1 (CI/RI values ≥ 0.7
to be accepted)
 Consistency Index (CI)
 Retention Index (RI)
2. Maximum Likelihood (ML) Analysis
 criterion-based approach
 preferred tree is the tree that has the
highest possibility of producing the
data we observe given a specific
model of evolution adopted by the
investigator
 Put together the taxa which has the
highest possibility of similarity following
a certain model of evolution.
 The values (numbers) found in an ML
tree are also called Bootstrap support
(BS) values.

1
SYSTEMATICS LAB
Values describe whether a that will be used to create
clade is strongly/ moderately/ organism’s phylogenetic tree
weakly supported  Still very useful especially in taxa with
 BS values > 85% are strongly no prior phylogenetic placements or
supported when the taxa only has a specific
3. Bayesian Inference (BI) or Bayesian Analysis gene region that can be readily
 Infers relationship by estimating the targeted and amplified.
probability of the tree topology
given the data and model (rather
than the probability of the data
given the model and tree topology
which is employed by ML)
 Posterior Probabilities (PP) ranges 0-1
 BI support values
 posterior probability of
phylogenies is approximated
by sampling trees from the
posterior probability
distribution
 uses algorithms known as
Markov chain Monte Carlo
(MCMC) or the Metropolis-
coupled Markov chain
Monte Carlo (MCMCMC).
 PP ≥ 0.95 strongly supported

Phylogenetic Softwares
1. Molecular Evolutionary Genetics Analysis
(MEGA)
 Provides conditions that allow initial
MP, ML and NJ analyses.
2. Phylogenetic Analysis using Parsimony
(PAUP)
 Conduct model search tests such as
MrModelTest and for maximum
parsimony analysis
3. MrBayes
 Software specialized for Bayesian
Inference
4. Randomized Axelerated Maximum
Likelihood (RAxML)
 Another software that specializes in
maximum likelihood analysis
5. CIPRES
 A free, open access engine that
allows to submit their aligned
sequences in specific phylogenetic
tasks.

Single-marker analysis
 Phylogenetic studies requires a single
set of molecular data to be used
 The sequence that can provide
reliable amount of informative data

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