lab 6 taxonomy

Introduction

Taxonomy is the classification (organization) of organisms into related groups. Very early on, scientists recognized
the importance of classifying or ranking organisms. In the 1700s, Carl Linnaeus (also known as Carl
von Linn� or Carolus Linnaeus) developed what is now known as the Linnaean Classification System.
At
the highest level in this system, everything in nature was divided into
three kingdoms: mineral, vegetable,
and animal. Linnaeus then ranked sequentially smaller groups within each
kingdom as class, order, genus,
species and variety. This contribution to science earned him the title
�The Father of Taxonomy�. His system is still, in an evolved form, used
today to classify living organisms.

Starting with domain, there is a continual increase in specificity as organisms are classified into smaller and
smaller categories (Figure 1).

Figure 1: As the classification level becomes more specific, less organisms are described until a single species is classified.

In other words, the categories get smaller in terms of the number of organisms
that are included. As illustrated in Figure 1, the Linnaean system classifies organisms into sequential groups:

• Domain
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species

Interestingly, there is not a consensus definition of
�species� among scientists at this time. The biological species
concept is the most commonly used definition. Basically
it defines a species as a group of individuals that can
interbreed and create viable offspring. Sub-species are
used in some classifications and is generally accepted, but
not always included in the Linnaean system.

A useful tool to remembering the order of the Linnaean
classification system is developed by creating a mnemonic phrase using
the first letter of each classification. For example, Daring Kids Pick Cauliflower Over Fresh Grown Strawberries. Can you create any mnemonics to help remember the Linnaean classification system?

Binomial Nomenclature

Carl Linnaeus also helped to standardize the naming of species by introducing the binomial (two name) species name. Binomial nomenclature uses
the genus and species as the formal name of all organisms because they
are the two most specific levels therefore unique to the organism. For
example, human beings are Homo sapiens. Note that the genus
is capitalized while species is not and, since these are Latin names,
they are italicized. Some organisms can have more than one common name
(i.e. cougar, puma and mountain lion). Using binomial nomenclature
specifies a species.

Advances in Taxonomy

Taxonomy is in a constant state of flux. Traditional groupings of organisms were dependent on mostly morphological
traits, physiological similarities and, to some extent, embryological events. Consider what techniques
were available in the 1700s when Carl Linnaeus described his system for ranking life. Gross anatomy
could be studied and identified, but most forms of microscopy were not available.

Phylogenetics

With advances in molecular techniques, nucleic acid (DNA) sequences are used to classify organisms
based on their evolutionary history. These advancements have given birth to the field of phylogenetics.
Phylogenetics is the field of study that determines the
evolutionary relationships among groups of organisms
using morphological traits, behavioral information and molecular data.
Ribosomal RNA (rRNA) is currently
one of the genes of choice for phylogenetic studies. rRNA is necessary
for the production of proteins and, because all life forms require
proteins, it follows that all organisms include rRNA genes. Sequences
from specific regions of an rRNA gene demonstrate similarities amongst
different organisms, enabling evolutionary
relationships to be explored. It is well accepted that the more similar
the sequences are between
two organisms, the more closely related the organisms. As DNA sequencing
techniques improve (and
costs decrease) other regions of the genome are also being sequenced and
compared.

Hot Topics in Taxonomy

Keep in mind that new techniques aid in classifications and, at
the same time, cause previously well accepted classifications to become
obsolete. Currently, many sources list three domains: Bacteria, Archaea,
and Eukarya. Within Eukarya are four kingdoms: Protista, Plantae,
Fungi, and Animalia. The Kingdom Protista has historically been a
�catch-all� category for all single-celled eukaryotic organisms; but,
not plants, fungi or animals. However, molecular data has revealed
distinct relationships within the eukaryotes that has led to new ideas
about classifying organisms into kingdoms and a new level called “supergroups”.
In this classification system, organisms that share a common ancestor
are grouped together and organisms that were previously placed in the
Kingdom Protista are distributed throughout new categories. Recall that
the organization of organisms based on shared common ancestors is
considered phylogeny. The “supergroups” are Excavata,
Amoebozoa, Opisthokonta, Rhizaria, Chromalveolata, and Archaeplastida.
In this organizational system, animals fall within Opisthokonta and
plants are placed in Archaeplastida.

Classifications will continue to evolve as scientists are able to delve at increasingly deeper molecular levels.
For now, the Kingdom Protista will continue to be used in this manual as we briefly survey the three
domains (Bacteria, Archaea and Eukarya) and four kingdoms (Protista, Plantae, Fungi, and Animalia).