Kevin C.

 Nixon, in Encyclopedia of Biodiversity, 2001

VII.D. Phylogeny and Biodiversity: Phylogenetic Diversity
Phylogenies also provide a framework for alternative ways of looking
at biodiversity. Most measures of biodiversity use species richness,
either in a geographic (either broad or local) or ecologic sense. Other
views of diversity may focus on the nature and breadth of adaptation.
Such measures unfortunately require a subjective view of the
importance of particular adaptations—e.g., the birds might be
considered “diverse” because they include so many adaptations for
use of the bill. However, phylogeny provides another perspective on
biodiversity that allows an objective way to compare uniqueness and
diversity of taxa. Although various specific measures
of phylogenetic diversity have been proposed, most share a basic
approach by which phylogenetic trees are used to evaluate species
richness in concordant groups. It means little to say that “orchids are
highly speciose” or “monotremes are species depauperate” unless we
have some idea as to the relationships of the two groups being
compared. Phylogenetic pattern provides the basis for such
comparisons.
Currently, the use of phylogenetic diversity measures is largely limited
to theoretical discussions and there have been few efforts to actually
apply such measures to conservation. This is partly due to the relative
paucity of high-quality phylogenies that are available across broad
groups of taxa and partly because of a distinctly ecological bias in
most studies of biodiversity. As molecular data sources provide better
and more complete phylogenies for use by other workers, this is likely
to change. It is probable that in the near future measures of
phylogenetic diversity will become standard components, in
combination with more traditional measures of ecologic uniqueness,
species richness, and sensitivity, in the formulae that are used to
evaluate conservation priorities for areas and endangered species.
View chapter Purchase book
Phylogeny
M. Charleston, in Brenner's Encyclopedia of Genetics (Second
Edition), 2013
Abstract
The branching pattern of ancestor–descendant relationships among
‘taxa’ (e.g., species or their genes) is called a ‘phylogeny’.
‘Phylogenetics’ is the process of attempting to estimate these
historical relationships by examining information such as DNA, protein
sequences, or morphological (shape) characters from extant taxa.
This information is generally presented using a mathematical tree – a
structure used to describe the evolutionary history of the taxa at a high
level. These trees come in several different varieties and can be
inferred in several different ways. There is a great amount of effort
being put into methods of estimating trees, as well as determining
particular phylogenies for species of interest.
View chapter Purchase book
Phylogeny
Alex A. Malone, Susan G. Larson, in Morrey's the Elbow and its
Disorders (Fifth Edition), 2018
Introduction
The human elbow forms the link between brachium and forearm,
controlling length of reach and orientation of the hand, and is one of
our most distinctive anatomic regions. An appreciation of
elbow phylogeny complements anatomic knowledge in three ways: (1)
it demonstrates how the elbow has evolved to facilitate specific
functional demands, such as suspensory locomotion and dexterous
manipulation; (2) it explains the functional significance of each
morphologic feature; and (3) it assists in predicting the consequences
of loss of such features through disease, injury, or treatment.
Most of the characteristic features of the human elbow significantly
predate the appearance of modern Homo sapiens. In fact, current
evidence suggests that this morphology can be traced back to the
common ancestor of humans and apes, extant approximately 15 to 20
million years ago (mya).
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Bioinformatics
P. Bawono, J. Heringa, in Comprehensive Biomedical Physics, 2014
6.07.4.1 Phylogenetic Analysis Using Parsimony
PAUP is a phylogenetic software package written by Wilgenbusch and
Swofford (2003). As the name implies, the earlier versions of PAUP
only employed the parsimony method. However, since version 4.0
(also known as PAUP*), the software package provides support for
distance-based and maximum likelihood methods as well. PAUP uses
a portable file format designed for systematic data called NEXUS
(Maddison et al., 1997). NEXUS is also supported by other
phylogenetic programs such as MacClade (Maddison and Maddison,
2000) and MrBayes (Huelsenbeck et al., 2001), which allow easy data
interchange between these programs. PAUP provides a graphical
user interface and a command-line interface for Macintosh and
Windows operating systems and only a command-line interface for
UNIX-like operating systems. The PAUP software package can be
downloaded from http://paup.csit.fsu.edu/about.html.
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Natural Product Biosynthesis by Microorganisms and Plants, Part C
Nadine Ziemert, Paul R. Jensen, in Methods in Enzymology, 2012
Abstract
Phylogenetics is the study of the evolutionary relatedness among
groups of organisms. Molecular phylogenetics uses sequence data to
infer these relationships for both organisms and the genes they
maintain. With the large amount of publicly available sequence data,
phylogenetic inference has become increasingly important in all fields
of biology. In the case of natural product research, phylogenetic
relationships are proving to be highlyinformative in terms of
delineating the architecture and function of the genes involved
in secondary
metabolite biosynthesis. Polyketide synthases and nonribosomal
peptide synthetases provide model examples in which individual
domain phylogenies display different predictive capacities, resolving
features ranging from substrate specificity to structural
motifs associated with the final metabolic product. This chapter
provides examples in which phylogeny has proven effective in terms
of predicting functional or structural aspects of secondary metabolism.
The basics of how to build a reliable phylogenetic tree are explained
along with information about programs and tools that can be used for
this purpose. Furthermore, it introduces the Natural Product Domain
Seeker, a recently developed Web tool that employs phylogenetic
logic to classify ketosynthase and condensation domains based on
established enzyme architecture and biochemical function.
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Phylogenetic Analysis: Early Evolution of Life
Himakshi Sarma, ... Sandeep Kaushik, in Encyclopedia of
Bioinformatics and Computational Biology, 2019
Tracing the Evolutionary Steps Using Phylogeny
Phylogeny can be described as the relationship between all the
organisms on Earth that have descended from a common ancestor,
whether they are extinct or extant. Phylogenetics is the science of
studying the evolutionary relatedness among biological groups and
a phylogenetic tree is used to graphically represent this evolutionary
relation related to the species of interest (Figs. 9–11).

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 Fig. 9 . Phylogenetic tree of contemporary organisms.

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Fig. 10 . Phylogenetic tree of bacteria.

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Fig. 11 . Elements of a typical phylogram.

More specialized phylogenetic methods have been developed now to

meet specific needs, such as species and molecular phylogenetic
tests, biogeographic hypotheses, testing, for evaluating amino acids of
extinct or extant proteins, establish disease epidemiology and
evolution, and even in forensic studies (Linder and Warnow, 2005).
View chapter Purchase book
Phylogenetic Invariants and Markov Invariants☆
P.D. Jarvis, ... J.G. Sumner, in Reference Module in Life Sciences,
2017
Abstract
“Phylogenetics” is the systematic study of reconstructing the past
evolutionary history of extant species or taxa, based on present-day
data, such as morphologies or molecular information (sequence data).
This evolutionary history or phylogeny is ideally represented as a
binary tree. In the method of “phylogenetic invariants,” a pivotal role is
played by certain master functions (the so-called invariants, which
give the method its name). The aim is to use the observed data as
input for their evaluation, and dependent on the answers, to infer
essential features of phylogenetic history without the need for
parameter estimation. We compare and contrast “phylogenetic
invariants” with “Markov invariants,” closely related quantities which
we have recently introduced in phylogenetics.
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Rehabilitation and Re-education (Movement) Approaches
Matthew Wallden ND DO, in Naturopathic Physical Medicine, 2008
Dimensional mastery
‘Phylontogenetic’ dimensions
Phylogeny is the development of species in general, while ontogeny
concerns the development of the individual. It is a commonly stated
that, as a loose rule, ontogeny recapitulates (or recaptures/mimics)
phylogeny (Heglund & Schepens 2003). This concept is illustrated in
any comparative anatomy or developmental biology text: ‘ontogeny
recapitulates phylogeny’.
Phylontogenetic dimensions can be defined as: ‘The emergent
movement patterns of the individual, in which the pattern of evolving
dimensional mastery of species is reflected.'
The detail of how such emergent movement patterns reflect the
dimensional mastery demonstrated throughout the fossil record, from
single-celled life to lower mammals, is described in the following
section ‘Phylogeny: dimensional mastery'.
View chapter Purchase book
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