Transcript Taxonomy and Phylogeny

Taxonomy
and
Phylogeny
and
Evolution
How do we as
biologists classify life?
What is taxonomy?
• Carolus Linnaeus [~1750s] began classifying
organisms based upon common morphological
characteristics. Ex: fur with four limbs, live birth,
warm blooded, animals are mammals
• He began the classification and naming system,
taxonomy, still used today but which has been
modified to rely heavily upon genetic information
to form a hypothetical arrangement of the
relationships between all species called
phylogeny.
• The modified version of the classification system
is named cladistics
Linneas’s taxonomy
• Began with a two kingdom system [animals and
plants] which was expanded into a 5 kingdom
system [animals, plants, monera, protists and fungi]
• Recently modified into a three domain system:
bacteria, archaea and eukarya
• Composed of a multilayered ladder of classification:
domain; kingdom, phylum, class, order, family,
genus and species. These are called taxa (plural) or
a single taxon
• Most organisms are referred to using their genus
and species: Ex: Homo sapien.
• The genus – Homo is always capitalized, the species
is not. The entire name is italicized. This is called
the binomial naming system originally developed by
Linnaeas and still used today.
The modern classification
• The modern system
uses three domains. All
organisms are classified
under one of these three
domains following the
usual Linnaean
classification system.
– Bacteria: no nucleus
– Archaea:
– Eukaryota
How does it work?
• Every organism has its own classification. Ex.
Humans are classified as follows:
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Domain:
Kingdom:
Phylum:
Class:
Order:
Family:
Genus:
Species:
Eukarya
Animalia
Chordata
Mammalia
Primata
Hominidae
Homo
sapien
nucleated cells
animal cells
develop with notochord
warm blood, live birth
thumb, collarbone,
S shape spine, bipedal,
evolutionary distinction
evolutionary distinction
Full details at:
http://www.cartage.org.lb/en/kids/science/Biology%20Cells/Studies/Human%20Taxonomy.htm
The bigger picture
• Scientists arrange these names into what are called
phylogenetic trees which show the evolutionary
relationship between all classified organisms. [In fact
most organisms have not been classified …yet!]
• The trees show structural and functional relationships
similar to the Linnaean system but also relies heavily
upon genetic and molecular evidence to support the
evolutionary ancestry. Linnaeus never had genetic
evidence to help him; he only had morphological and
behavioural evidence [I.e structural]
NOTE!!
• Lets check this out in more detail….
http://evolution.berkeley.edu/evosite/evo101/IIAFamilytree.shtml
• Notice that the modern classification system is NOT
anthrocentric, we are just one species in the system!
The 3 new domains
• Bacteria: classified as anucleated,
peptidoglycan cell wall, circular chromosome –
no histones, almost all unicellular, ribosomes
and RNA polymerase different from
• Archaea: have polysaccharide cell walls,
circular chromosome with histones, all known
are unicellular, ribosomes and RNA
polymerase similar to
• Eukarya: membrane bound nucleus, linear
chromosomes with histones, multicellular,
Previous hypothesis:
• Based upon morphology, the structural forms
and shapes, of Bacteria and Archaea it was
expected that the Archaea and Bacteria were
more closely related – had the most recent
common ancestor – than Archaea and
Eukarya. Hence a basic phylogenetic tree like:
• Bacteria
Archaea
Eukarya
Common ancestor
Between Bacteria and
Archaea
-a speciation event
common ancestor to all three
-also a speciation event
New hypothesis – for now:
• However ,with the ability to sequence genomes
cheaply and efficiently and collect detailed
molecular data the evolutionary genetic
evidence supports the hypothesis that Archaea
and Eukarya share the more common
ancestor, not Bacteria and Archaea.
• Draw the phylogenetic tree that would suggest
this hypothesis.
• Is this the final word?? How does this topic
reflect the nature of science?
• Check these out!
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http://www.genome.org/cgi/content/full/9/6/550
http://www.sciencemag.org/cgi/content/summary/280/5364/672?rbfvrToke
n=97e2629b909a2608b07659608907897d6e836d73
Deeper Phylogeny
• A clade is an evolutionary branch on the tree
which represents an ancestor and ALL its
decendents.
Evolution without speciation
Evolution with a population
Undergoing speciation
This is called a node.
Other ancestral relationships:
• A true clade is referred to as monophyletic if it meets the proper
criteria – an ancestor and ALL its decendents.
• Paraphyletic relationship is not considered a clade. It is an
ancestor and only some of its decendents.
• Polyphyletic is also not a true clade (think branch), it is used to
describe a group with more than one ancestral founder. [C, F]
– Note: remember that poly is latin for ‘many’
Continued…
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Sharks evolve but do not
undergo speciation
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At this time the ancestor of sharks underwent
speciation causing two species to form. One of
the species continued to evolve into sharks
that have a cartilaginous skeleton. The other
species evolved a bony calcaneous type of
skeleton. This second species continued to
evolve into split populations forming new
species that continued to evolve new traits of
species we are familiar with.
Q. Using the previous terms, describe the relationship between:
a) Sharks, and primates. b) Primates and rodents. c) Primates, rodents, crocs and
birds.
Phylogeny relates to Evolution.
• Obviously the new taxonomic cladistic
relationships are heavily dependent upon
evolutionary relationships based upon
morphological, behavioural, genetic and
molecular data.
• But!  What is the evolutionary
process?
Evolutionary Basics: Ch 22
• Central tenet: All life on earth shares a common
ancestor. Hey – thats the cladistic organization! Cool
huh 
• There are four basic accepted parts to evolutionary
theory:
Point form
– Variation: All populations vary genetically, selection between
these individuals within the population is due to these
variations. [the genetic variation leads to phenotypic variation]
– Inheritence: The genetic variations are inherited from parents
and passed onto offspring.
– Selection: The genetic variations lead to phenotypic
differences within the population and confers varying levels of
organism success [survival/reproductive success].
– Time: evolution takes time. From days in rapidly reproducing
organisms [Bacteria/Archaea] to millennium for long lived
species [many Eukarya]
Evo - continued
• If you prefer a narrative:
– “In biological phrasing, the genotype has been
altered by one of these forms of mutation or
another, and as a result there is now a different
phenotype. New phenotypes, or altered traits in
anatomy, physiology or behaviour, usually have
some effect on survival and reproduction. If the
effect is favourable the mutant genes prescribing
them proceed to spread through the population. If
the effect is unfavourable, the prescribing genes
decline and may disappear altogether.”
» Pg. 80. Diversity of life. Edward O. Wilson
• Here is an example of lizards in the Caribbean.
Appendix A: Important terms
• Taxonomy: the use of organism characteristics to
classify organisms from kingdom to species.
• Phylogeny: the use of genetic evolutionary
relationships to create an ancestral tree of evolution.
• Cladistics: The analysis of how species are
organized into ancestral relationships
• Protists: eukaryotic organisms that are not an
animal, green planet or fungi
• Monera: prokaryotic organisms such as bacteria ad
archeabacteria
• Speciation: the splitting of a population of
organisms into two differernt distinct groups that are
unable to mate successfully
• A node is a location in a phylogeny where a
speciation event has occurred
• Population: a collection of organisms of the same
species
• Genotype: the genetic [DNA] composition of an
organism
• Phenotype: the physical/physiological traits of an
organism
Appendix B: Warning! 
• Be careful! During this course we will delve deeper into
the study of evolution. We will find the following
occurs..
• A phylogenetic tree shows the evolutionary genetic
relationship between ancestors and the species
descended from the ancestor. As a result it is very
likely that species with similar characteristics share a
close ancestor and therefore have very similar
genomes.
• However, and this is the beware part, organisms may
develop similar physical [etc] characteristics without a
close ancestor due to convergent evolution.
Convergent evolution occurs when evolutionary
unrelated species have similar characteristics because
of similar lines of evolutionary selection. Ex. Placental
wolf of Europe/North America vs. the marsupial wolf of
Australia.
Cladogram
Dichotomous Key
Blue Whale
Animalia
Plantae
Chordata
Coniferophyt
a
Mammalia
Pinopsida
Cetacea
Balaenopterida Pinales
e
Taxodiaceae
Balaenoptera Sequoia
musculus
semperviren
King Phillip Came Over For Good
s Supper
Gross Sometimes
Kingdom
Phylum
Class
Order
Family
Genus
Species
Coast Redwood
Kissing Pretty Cute Otter Feels
King Phillip Came Over For Good Soup