In determining evolutionary relationships and constructing family trees, cladistics is the most
commonly used method. Its use has helped advance science in many areas, including
anthropology and botany, as well as understanding how life evolved. As DNA technology has
advanced, so has the understanding of how organisms change over time. In addition to this,
cladistics is an important tool for the study of small fossils and extinct species.
Molecular data are easily converted to numerical form
DNA is a four billion year old biological molecule that stores genetic information. It is made up
of four molecules, called nucleotides. The letters A, T, C, and G stand for Adenine, Thymine,
Cytosine, and Guanine. DNA is an extremely durable storage medium because it can withstand
hundreds of thousands of years without energy input. It can be protected from light, water, and
temperature. DNA is a million times more compact than conventional storage media, with a
density of 450 million TB 2 per gram. It is so dense that all the data in the world would fit in
the volume of a chocolate bar.
Using DNA synthesis technology, scientists can quickly generate large libraries of genomes,
which are then subjected to screening and selection to achieve desired traits. This can lead to
a variety of advancements in genetic research, including the sequencing of the human
genome. Because DNA is so easily translated to numerical form, scientists can create
genetically accurate maps of a specific organism’s entire genome.
Maximum parsimony is a concept used by scientists to
describe phylogenetic analysis
Phylogenetic analysis uses a method of tree-estimation known as maximum parsimony.
Maximum parsimony involves scoring trees based on their parsimonious distribution of
character data. The most parsimonious tree is deemed the best estimate of phylogenetic
relationships among taxa. However, there is no universally accepted definition of phylogenetic
character.
When using maximum parsimony in phylogenetic analysis, the number of taxa included in the
tree must be kept to a minimum. The more taxa in the tree, the more time it takes to estimate
the branches, which leads to a higher degree of uncertainty. Data collection costs scale
directly with the number of taxa included in the analysis. Hence, most analyses contain only a
few taxa. Furthermore, if the number of taxa is relatively small, the method known as branch-
and-bound guarantees the best tree.
Scientists use the concept of maximum parsimony to select competing models in phylogenetic
analysis. This principle focuses on the simplest explanation for a particular event. For
example, when estimating the distance between two species, they need to consider the least
amount of characters and mutations. The most closely related pairs of taxa are found on either
side of the internode.
Another way to calculate maximum parsimony is to model the evolution of an individual gene
or a single site with a phylogenetic network. The resulting phylogenetic network is the
combination of the species tree and the gene tree, with the two being modeled by a single
network. In the maximum parsimony model, different substitutions don’t contribute equally to
the parsimony score.
As long as each clade has a common ancestor, a cladist’s hypothesis is more likely to be
correct. In fact, maximum parsimony has been widely adopted by scientists to describe
phylogenetic analysis. In principle, maximum parsimony can be used to identify the highest
level of a monophyletic group.
This technique has been widely adopted since it was introduced and continues to be used
today. Maximum parsimony relies on the premise that evolution is parsimonious. In other
words, the best evolutionary tree is characterized by minimum mutations or the least number
of changes in branches. Maximum parsimony has been applied to various data sets for nearly
30 years and is the most widely used method for phylogeny reconstruction.
Using this method, scientists can build a genetic trait tree by considering all possible
relationships between species. Among the possible relationships, they select the one with the
fewest number of state changes. They continue this process until they find a common ancestor
of all species. If an evolutionary relationship cannot be explained by an intermediate ancestor,
it is considered incorrect.
A key principle of maximum parsimony is that all similarities between two species are
homologous. When comparing two species, the likelihood of a branch being closer than
another is greater. A parsimony-based approach relying on characters is more likely to be
unbiased. However, there is no universal maximum parsimony, so the methods that work best
for phylogenetic analysis are not necessarily better than those that rely on a combination of
the two.
The MP problem is defined as “finding an MP phylogenetic tree T for a set S” (dataset S). It is
NP-hard and becomes even harder if sequences are binary. For example, in a 40-taxon data
set, the optimal improvement in parsimony score is greater than 80 points. However, when
analyzing a 46-taxon dataset, the optimal parsimony improvement is higher than 80 points.
Phylogenetic trees are made by identifying homologous genes and characteristics. The
similarities between organisms may result from shared evolutionary history or from separate
paths. New technologies have helped scientists distinguish between analogies and
homologies. By applying cladistics to phylogenetic information, scientists can reconstruct the
evolutionary timeline and use the principle of maximum parsimony to determine which of two
species is closer to being most similar.
In phylogenetics, the bootstrap method is more commonly used. This method consists of
perturbation of data and analysis of the resulting MPTs. The results are usually presented on a
50% Majority Rule Consensus tree with individual branches labeled with the bootstrap
percentage. Note that the bootstrap percentage is not a P-value; instead, it serves as a
measure of support and repeatability.
