Taxonomy and Phylogenyand 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:• Domain: Eukarya nucleated cells• Kingdom: Animalia animal cells• Phylum: Chordata develop with notochord• Class: Mammalia warm blood, live birth• Order: Primata thumb, collarbone, • Family: Hominidae S shape spine, bipedal, • Genus: Homo evolutionary distinction• Species: sapien evolutionary distinctionFull 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] NOTO!!

• 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! • http://www.genome.org/cgi/content/full/9/6/550• http://www.sciencemag.org/cgi/content/summary/280/5364/672?

rbfvrToken=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…

• Sharks evolve but do not • undergo speciation

• 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

Kingdom

Phylum

Class

Order

Family

Genus

Species

Animalia

Chordata

Mammalia

Cetacea

Balaenopteridae

Balaenoptera

musculus

Plantae

Coniferophyta

Pinopsida

Pinales

Taxodiaceae

Sequoia

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