KEGS Biology Blog


Year 13 1st March
March 1, 2013, 11:48 pm
Filed under: Uncategorized

Cladistics

Advertisements

5 Comments so far
Leave a comment

Cladistics is an advanced method of assessing the phylogenic relationships between organisms and ascertaining the evolutionary development of a species. The cladistics definition of a species is as follows:

‘A species is a set of organisms (an evolutionary lineage) between two branch points or between one branch point and an extinction event or a modern population (Ridley 1993)’

This can be more easily understood in the context of a cladogram, a common diagrammatic representation of the phylogenic relationship between organisms. The main difference between a cladogram and a normal evolutionary diagram is that a cladogram displays organisms only as end-points, rather than intermediate stages. Evolutionary developments (e.g. a mutation of development of fur) is displayed as a point in evolutionary history and hence shows the instant at which it developed, instead of showing a gradual development.

Cladistics therefore groups organisms by their synapomorphies (shared derived characteristics), much like an evolutionary tree. The above definition of cladistics in relation to cladograms is very useful, however, when we think about organisms that reproduce asexually (and hence cannot be defined by the usual biological definition of species).

A very useful link I found in explaining cladistics I have added below, however a very useful paragraph I found as to the benefits and need of cladistics I have added below as well:

‘Unlike previous systems of analyzing relationships, cladistics is explicitly evolutionary. Because of this it is possible to examine the way in which characters change within groups over time — the direction in which characters change, and the relative frequency with which they change. It is also possible to compare the descendants of a single ancestor to look at patterns of origin and extinction in these groups, or to look at relative size and diversity of the groups. Perhaps the most important feature of cladistic is its use in testing long-standing hypotheses about adaptation. For many years, since even before Darwin, it has been popular to tell “stories” about how certain traits of organisms came to be [I assume this refers to people noticing gradual changes in our ancestor organisms with geological time, as although mutations themselves are instant, the impact and process of natural selection takes much longer]. With cladistics, it is possible to determine whether these stories have merit, or whether they should be abandoned in favor of a competing hypothesis. For instance, it was long said that the orb-weaving spiders, with their intricate and orderly webs, had evolved from spiders with cobweb-like webs. The cladistic analysis of these spiders showed that, in fact, orb-weaving was the primitive state, and that cobweb-weaving had evolved from spiders with more orderly webs. This situation has been repeated in many groups with many traits, including studies of parasitism, geographic distribution, and pollination.’

Source and very useful link: http://www.ucmp.berkeley.edu/clad/clad1.html

Comment by jonathanfunnell

Intro video: http://www.youtube.com/watch?v=3DxNwzzjm_4

Cladistics is a method of classifying plants and animals according to the proportion of measurable shared derived characteristics. The idea behind cladistics is that members of a group share a common evolutionary history, more so to members of the same group than to other organisms. These groups are recognised by sharing unique features, which were not present in distant ancestors. These shared derived characteristics are called synapomorphies. Note that is not enough for organisms to share characteristics.

Cladistics is the method of choice for classifying life because it recognises and employs evolutionary theory. By doing so, cladistics can examine the way in which characters change within group over time. This gives this model the ability to compare the descendants of a single ancestor to look at patterns of origin and extinction in these groups.

In addition, it produces hypotheses about the relationships of organisms in a way that predicts properties of the organisms. This can be especially useful when particular genes or compounds are being sought.

Perhaps the most important feature of cladistics is its use in testing long standing hypotheses about adaptation.

Here is an outline of the steps necessary for completing a cladistic analysis. Don’t be fooled, however, by the simplicity of these steps. Seeing a real cladistic analysis out to fruition can be a difficult and time consuming task.
1. Choose the taxa whose evoutionary relationships interest you.
2. Determine the characters (features of the organisms) and examine each taxon to determine whether each taxon does or does not have each character.
3. Determine whether each character state is original or derived in each taxon.
4. Group taxa by synapomorphies (shared derived characteristics)
5. Work out conflicts that arise by some clearly stated method, usually parsimony(minimizing the number of conflicts).
6. Build your cladogram (Jon’s top link)
There are three basic assumptions in cladistics:
1. Any group of organisms are related by descent from a common ancestor.
2. There is a bifurcating pattern of cladogenesis.
3. Change in characteristics occurs in lineages over time.
The first assumption is a general assumption made for all evolutionary biology. It essentially means that life arose on earth only once, and therefore all organisms are related in some way or other. Because of this, we can take any collection of organisms and determine a meaningful pattern of relationships, provided we have the right kind of information. Again, the assumption states that all the diversity of life on earth has been produced through the reproduction of existing organisms.
The second assumption is perhaps the most controversial; that is, that new kinds of organisms may arise when existing species or populations divide into exactly two groups. There are many biologists who hold that multiple new lineages can arise from a single originating population at the same time, or near enough in time to be indistinguishable from such an event. While this model could conceivably occur, it is not currently known how often this has actually happened. The other objection raised against this assumption is the possibility of interbreeding between distinct groups. This, however, is a general problem of reconstructing evolutionary history, and although it cannot currently be handled well by cladistic methods, no other system has yet been devised which accounts for it.
The final assumption, that characteristics of organisms change over time, is the most important assumption in cladistics. It is only when characteristics change that we are able to recognize different lineages or groups. The convention is to call the “original” state of the characteristic plesiomorphic and the “changed” state apomorphic.

Questions
What are synapomorphies?
What can cladistics predict?
What are the three assumptions in cladistics?

Comment by benjamincharlespatterson

The traditional definition of a species, under the biological species concept, is ‘a group of
similar organisms which are able to interbreed to successfully to produce viable (fertile)
offspring.’ However, there are several problems with this definition:
– Not all ‘species’ interbreed in the wild, so we do not know whether they would
produce viable offspring.
– Not all possible crosses can be tested in the lab (e.g. crossing a human and a chimp)
– Some species are extinct so we cannot investigate their mating behaviour
– Some unrelated organisms can look very similar, without being members of the same
species
– Not all organisms reproduce sexually (e.g. bacteria)
As a result of these problems, we sometimes use the phylogenetic species concept, which
defines a species as: ‘a group of organisms with similar morphology, physiology,
embryology and behaviour, and occupy the same ecological niche.’ This concept involved
studying the evolutionary history of a group of organisms, to see how genetically similar to
another group of organisms they may be. All organisms evolved from a common ancestor,
and the more recently the groups diverged away from each other, the more closely related
they are. The phylogenetic linkage is called a ‘clade.’ However, this theory also has issues:
– There is no definitive ‘cut off point’ at which point two groups can be
established as the same species (e.g. humans and chimps share 94% of the same
DNA)

Comment by aliciacork

Put together by Hassan Khan and Hamza Mahmud
Cladistics is a type of phylogenetic nomenclature designed to more accurately place organisms into different clades based on evolutionary relationships. It is preferred to the mostly anatomical method of classification because it is based on much more detailed evolutionary trees which are called cladograms.
Merriam-Webstier defines cladistics as ‘a system of biological taxonomy that defines taxa uniquely by shared characteristics not found in ancestral groups and uses inferred evolutionary relationships to arrange taxa in a branching hierarchy such that all members of a given taxon have the same ancestors’. It may be useful to use this for a more accurate definition as opposed to the one before.
An example of a basic one can be seen here: http://schoolworkhelper.net/wp-content/uploads/2010/12/cladogram.gif
A less visual but more detailed one: http://upload.wikimedia.org/wikipedia/commons/a/a5/The_Ancestors_Tale_Mammals_cladogram.png
The first cladogram shows that certain characteristics belong to all species mentioned which in this case is ‘Vertebrae’. This ancestral trait is called symplesiomorphic and the organism originating that trait can be described as plesiomorphic. When referring to organisms on the more evolved end of the cladogram, they can be called apomorphic or derived organisms.
There are three basic assumptions which provide the basis for cladistics:
1. Any group of organisms are related by descent from a common ancestor.
2. There is a bifurcating pattern of cladogenesis.
3. Change in characteristics occurs in lineages over time.
The website linked below this explains the definitions very well
‘The first assumption is a general assumption made for all evolutionary biology. It essentially means that life arose on earth only once, and therefore all organisms are related in some way or other. Because of this, we can take any collection of organisms and determine a meaningful pattern of relationships, provided we have the right kind of information. Again, the assumption states that all the diversity of life on earth has been produced through the reproduction of existing organisms.
The second assumption is perhaps the most controversial; that is, that new kinds of organisms may arise when existing species or populations divide into exactly two groups. There are many biologists who hold that multiple new lineages can arise from a single originating population at the same time, or near enough in time to be indistinguishable from such an event. While this model could conceivably occur, it is not currently known how often this has actually happened. The other objection raised against this assumption is the possibility of interbreeding between distinct groups. This, however, is a general problem of reconstructing evolutionary history, and although it cannot currently be handled well by cladistic methods, no other system has yet been devised which accounts for it.

The final assumption, that characteristics of organisms change over time, is the most important assumption in cladistics. It is only when characteristics change that we are able to recognize different lineages or groups. The convention is to call the “original” state of the characteristic plesiomorphic and the “changed” state apomorphic. The terms “primitive” and “derived” have also been used for these states, but they are often avoided by cladists, since those terms have been much abused in the past.’
Questions:
Use the following image to answer the questions: http://thestagecoachroad.files.wordpress.com/2013/01/mammal-cladogram-the-tree-of-life-evolutio-15.gif?w=500&h=336
1. Name a plesiomorphic organism when compared to a Salamander.
2. Name an apomorphic organism when compared to a Lizard.
3. Which organism can be described as a derived organism?

Comment by hasssankhan

Cladistics is the hierarchical classification of species, based on their evolutionary ancestry. Like other methods, it has its own set of assumptions, procedures, and limitations. Cladistics is now accepted as the best method available for phylogenetic analysis, for it provides an explicit and testable hypothesis of organismal relationships.

The basic idea behind cladistics is that members of a group share a common evolutionary history, and are closely related, more so to members of the same group than to other organisms. These groups are recognized by sharing unique features which were not present in distant ancestors.
It is different from taxonomic classification systems as:
– It focuses on evolution (phylogenetic relationships), rather than on similarities between species
– It places great importance on using objective and quantitative (molecular) analysis
– It uses DNA and RNA sequencing
– It uses computer programmes and the data obtained from nucleic acid sequencing to generate dendrograms or cladograms that represent the evolutionary tree of life, because manual creation of such diagrams would be extremely difficult when dealing with large numbers of species
– It makes no distinction between extinct and extant species and both may be included in cladograms

Feel free to follow the link below if you want to create your own cladogram or just see how they work!

http://ccl.northwestern.edu/simevolution/obonu/cladograms/Open-This-File.swf

The Linnaean system is a particular form of taxonomy set up by Carl Linnaeus. In the taxonomy of Linnaeus there are kingdoms, divided into classes, and they, in turn, into orders, families, genus and species. Cladistics is different from Linnaean classification because it does not use the groups kingdom, phylum or class as it regards the evolutionary tree as very complex. As such, it is not helpful to use a fixed number of levels in the classification of living organisms.

However, the Linnaean system of classification also reflects the phylogenies (evolutionary relationships) between the different species of organisms. But, unlike cladistics, it shows both monophyletic and paraphyletic groups as taxa.

The cladistic approach has often confirmed the Linnaean classification of organisms but has sometimes led to organisms being reclassified. It has helped biologists to understand the evolutionary relationships between species.

A paraphyletic group includes the most recent ancestor but not all its descendants. It is a monophyletic group with one or more clades excluded. For example, the grouping of reptiles is paraphyletic as it excludes bird, which are descendants of reptiles. The group Prokaryotes is paraphyletic as it comprises bacteria (eubacteria) and Archaea (Archaebacteria) but excludes.

Comment by ebelen




Leave a Reply

Please log in using one of these methods to post your comment:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s



%d bloggers like this: