Classification of Living Things

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Classification of Living Things

• Taxonomy - The science of classifying and naming
  organisms.

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• Throughout time, scientists have puzzled over how
  to group organisms. . .
• Do you put insects, birds, and bats together
  because they fly?
• How about putting squid, whales and fish together
  because they swim?
• It was during Renaissance times that people
  started to categorize creatures according to
  their similarities. The best system was
  developed by Carolus Linneaus around 1750. This
  system has been modified some, but is still in
  use. Linneaus did not know about evolution, and
  that concept is now incorporated in the
  classification system.

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Linneaus developed a binomial system of
nomenclature - two part names for organisms.
Organisms are identified by their Genus species
name. The names are given in Latin which is an
international language that is no longer in use.
This language can provide very specific names.
It removes ambiguity. Canis familiaris - is the
scientific name for domestic dogs of all breeds
in all parts of the world.
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• TAXONOMIC CLASSIFICATION IS HIERARCHIAL
• Domain Eukaryotic
• Kingdom Animalia
• Phylum (or Division) Chordata
• Subphylum Vertebrata
• Class Mammalia
• Order Primate
• Family Hominidae
• Genus Homo
• Species sapiens

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When working with a classification system, some
definitions are in order. . . A Taxon is a
particular taxonomic grouping (e.g. Chordata,
Mammalia) Subspecies (varieties, strains) - These
are geographically distinct populations with a
species often displaying certain consistent
characteristics that distinguish them from other
populations of the same species. Subspecies are
capable of interbreeding, however if they are
reproductively isolated they may, in time, become
clear-cut species.
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Splitters and Lumpers. . . Some organisms are
easy to classify, others are difficult. Lumpers
are taxonomists that group organisms into already
existing units recognize 10 animal phyla and 4
plant divisions.
You gotta know, Im a Lumper
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• Splitters - taxonomists that establish separate
  categories for organisms that do not fall
  naturally into an existing classification
  recognize up to 33 animal phyla and up to 12
  plant divisions.
• http//www.ncbi.nlm.nih.gov/sites/entrez?dbtaxono
  my
• The Domains - taxonomic categories larger than
  Kingdoms.
• Bacteria- Kingdom Eubacteria (bacteria and
  cyanobacteria) lack a nucleus and membranous
  organelles.
• Archaea - Archaebacteria
• Eukarya - Kingdom Protista, Fungi, Plantae, and
  Animalia have cells with distinct nucleus and
  membranous organelles.
• In some sources, biologists still recognize five
  Kingdoms.
• Newer classification systems are recognizing
  three domains or six Kingdoms

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• Classification is an ongoing area of research and
  discussion. As new findings and technologies
  become available they allow the refinement of the
  model. For example, gene sequencing techniques
  allow the comparison of the genome of different
  groups ( Phylogenomics ).
• Such a study published in 2007 by Fabien Burki,
  et al9 proposes four high level groups of
  eukaryotes based on Phylogenomics research.
• Plantae (green and red algae, and plants)
• Opisthokonts (amoebas, fungi, and all animals)
• Excavata (free-living and parasitic protists)
• SAR (an abbreviation of Stramenopiles,
  Alveolates, and Rhizaria, the names of some of
  its members. Burki found that the previously
  split groups Rhizaria and Chromalveolates were
  more similar in 123 common genes than once
  thought.)
• http//en.wikipedia.org/wiki/Kingdom_28biology29
  Recent_Advances

Ms. B
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Various classification systems that have been
used
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Systematics is the study of evolutionary
relationships - phylogeny. Monophyletic taxon -
this is a taxonomic grouping where all of the
subgroups have a common ancestry. A Clade is a
monophyletic taxon containing all species
descended from the common ancestor.
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Polyphyletic taxon is a taxonomic group in which
the subgroups do not share a common ancestry.
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Determining phyletic taxon. . . Homologous
structures imply divergent evolution from a
common ancestor. The relationship of organisms
is based on the extent of similarity between
living species and on the fossil
record. Homologous structures are important in
determining similarity they are a result of
divergent evolution. (Analogous structures result
from convergent evolution and are not as useful
when determining taxa.)
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Primitive and Derived characters. . . Primitive
characters are common to a group of organisms,
have remained essentially unchanged and indicate
a remote common ancestry. Derived characters are
those that have evolved more recently and
indicate a more recent common ancestry. Example
Three bones in middle ear - not all chordates
have them so they are a derived character in
chordates. All mammals have these three bones -
so they are a primitive character in
mammals. Primitive and Derived are relative
terms, in other words - a feature viewed as a
derived character in a large group may be seen as
a primitive character in a smaller taxon.
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• Choosing taxonomic criteria. . .
• Organisms are not grouped together that share
  analogous adaptations.
• Organisms are grouped together that share derived
  characteristics.
• Shared primitive characteristics serve as a basis
  for classification and indicate a common
  ancestry.
• Deciding the appropriate weights for various
  traits in determining taxonomic categories is not
  always simple.
• Organisms are usually classified by a combination
  of traits.
• DNA analysis is becoming an important component
  for classifying organisms.
• Taxonomy is a dynamic science.

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• Molecular Biology as a taxonomic tool. . .
• DNA evolution
• DNA evolves at a constant rate enabling
  biologists to use specific genes as molecular
  clocks.
• The number of differences in nucleotide sequences
  in two groups of organisms reflects the time
  since the groups branched off from a common
  ancestor.

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Phylogenetic analysis of CTCF-like candidates in
multiple species. Dendrogram of a
neighbor-joining consensus tree of 5000 bootstrap
replicates for an alignment of the 11 ZF region
of known and predicted CTCFs. The tree topology
is consistent with the taxonomic classification
of all Drosophila species. Gray and Coates BMC
Molecular Biology 2005 616   doi10.1186/1471-219
9-6-16
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• Protein evolution
• A given protein evolves at a constant rate
  enabling biologists to use specific proteins as
  molecular clocks.
• The degree of difference in amino acid sequence
  reflects the time that has passed since the
  groups diverged.

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• Protein Similarities. . .
• These can be determined by serological techniques
  that involve the immunological comparison of
  proteins. (The rabbit injected with rat blood
  example.)
• The amino acid sequencing techniques are more
  reliable.

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• DNA similarities. . .
• Among related species, the DNA sequences of the
  same structural genes are very similar.
• Detailed restriction maps within large homologous
  regions of chromosomes are also very similar.
• The genome of mammals consists of thousands of
  copies of alu-DNA differences in alu-DNA, even
  between closely related species are thought to
  reflect evolutionary changes.
• Hybridization techniques are used to compare DNA
  from different organisms.

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• There are three main approaches to taxonomy -
  phenetics, cladistics, and classical evolutionary
  taxonomy.
• The phenetic system is a numerical taxonomy in
  which organisms are grouped according to the
  number of phenotypic characteristics they share.
• Both homologous and analogous adaptations are
  computed.
• Evolutionary history is not reconstructed.
• Least popular method because it does not work
  very well.

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• The Cladistic approach emphasizes phylogeny,
  focusing on how long ago one group branched off
  from another. The taxa are monophyletic.
• This approach involves the construction of a
  diagram called a cladogram.
• The cladogram resembles a tree with organisms
  branching off at respective times delineating
  between primitive and derived characters.
• There are some problems with accuracy with this
  method. There is evidence that some branches of
  cladograms may be anecdotal examples.
• (Cladistics would classify birds with crocodiles
  due to common ancestry).

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Cladistics is really gaining popularity, and
throw in molecular biology as part of the
classification system and this really stirs
things up
http//www.ncbi.nlm.nih.gov/sites/entrez?dbtaxono
my
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A phylogenetic Tree constructed with Cladistics
http//www.talkorigins.org/faqs/comdesc/phylo.html

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• Classical Evolutionary Taxonomy has been the most
  widely accepted taxonomic system of phylogenetic
  classification.
• This system is based on evolutionary
  relationships and believe the degree of genetic
  differences between lineages should be used in
  addition to their genealogical (evolutionary)
  similarities when developing taxonomic
  classifications
• Organisms are classified in the same category
  according to their shared characteristics only if
  those traits are derived from a demonstrable
  common ancestor. (If they are monophyletic or
  paraphyletic).

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• The significance of the adaptations possessed by
  related organisms is also considered.
• The classical taxonomist is more of a splitter
  than a lumper.

A cladist would insist that crocodiles and birds
be placed in the same taxon, even though the
amount of change from the common ancestor is much
greater for the birds than it is for the
crocodiles. An evolutionary taxonomist would
suggest that the large number of similarities
between crocodilians and reptiles would justify
grouping them within the same general taxon,
while placing birds in a separate taxon due to
the large number of unique characters possessed
by members of this group.
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References
http//www.ncbi.nlm.nih.gov/sites/entrez?dbtaxono
my
http//www.mun.ca/biology/scarr/Taxon_types.htm
http//www.mhhe.com/biosci/pae/zoology/cladogram/