User:Arthur.181/sandbox

My topic involves the Methods of Study of Cladogenesis and what goes into separating different species and how scientists go about doing that.

Ree, Richard H., and Stephen A. Smith. "Systematic Biology." Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis. Oxford Journals, 29 Aug. 2007. Web. 07 Sept. 2014.

Mayr E (1947) Ecological factors in speciation. Evolution 1: 263–288.

Fortey, R. A., D. E.G. Briggs, and M. A. Wills. "The Cambrian Evolutionary ‘explosion’: Decoupling Cladogenesis from Morphological Disparity." Wiley Online Library. Biological Journal of the Linnean Society, 14 Jan. 2008. Web. 08 Sept. 2014.

Timothy G. Barraclough, James E. Hogan, and Alfried P. Vogler. "Testing whether ecological factors promote cladogenesis in a group of tiger beetles (Coleoptera: Cicindelidae)". Proc R Soc B 1999 266: 1061-1067.

Ronquist, Fredrik, and Isabel Sanmartin. "Phylogenetic Methods in Biogeography." Annual Review of Ecology, Evolution, and Systematics, 42(1):441. Department of Biodiversity Informatics, Swedish Museum of Natural History, 29 Aug. 2011. Web. 13 Sept. 2014.

Wikipedia Edit
There are many different methods and forms of evidence that can be used when it comes to studying whether or not a speciation event falls under cladogenesis or not. Below are a few different methods that are used by scientists to test whether or not something is a cladogenetic event with a quick explanation or example of how that method is/can be used in modern science: - Simulations: This involves the process of taking already known information (such as mitochondrial information) about a species and running the information through a computer to see if a cladogenetic event is the most probable explanation for a species existence. This way of studying species is the most practical. A lot of times, case studies and constructing experiments can cost a lot of money and takes time, so it is easier to plug information into a computer and allow the computer to run different scenarios to test for accuracy. - Morphological Evidence: Using fossil evidence can determine whether or not two species were alive at the same time. However, there are some drawbacks to using just fossil evidence, because fossil evidence can only differentiate species on an assemblage level. - Molecular Evidence: Molecular data can be used to see how the genome or DNA of specific species has diverged. This, along with the fossil evidence, can be a good basis for seeing if two distinct species came from a similar ancestral species and if they were both alive at the same time. - Models: This involves taking already alive species and running experiments (simulating possible environments for example) to see if speciation occurs in order to explain the presence of different species or if there is an alternate explanation for the species. This is sometimes the most accurate way of measuring speciation because it gives actual life results, as opposed to computer generated data. These are just a few examples of ways to try and distinguish a speciation event as cladogenetic or even possibly anagenetic. Scientists are constantly coming up with new ways to try and study species and determine how they are related to each other and what may have caused their splitting. https://en.wikipedia.org/wiki/Cladogenesis

This is where my Final Draft Starts
Methods of Study for Cladogenesis Trying to understand how certain species come about and evolve can often be a very tedious or even complicated task for scientists. Cladogenesis as the process in which a species diverges into two isolated species. However, these two species are still able to reproduce and evolve on their own. (Strotz and Allen 2012) Cladogenesis is a very interesting topic to study amongst scientists, even though there is no specific  way to go about studying whether or not something would be considered cladogenetic or not. There are numerous different ways that possible cladogenetic events can be studied. A majority of these methods require many years of study and numerous amounts of mathematical equations. Some basic methods that many scientists go about trying to study cladogenetic events are: using simulations, using morphological evidence (fossil records), using molecular evidence, and using models (such as the equal-rates markov model and dispersal-extinction-cladogenesis model). However, just one method alone isn’t enough to give enough evidence in order to make a steady argument for cladogenesis. For example, fossil records used by themselves, can only be used to make distinctions at the assemblage level, and that can make telling two different species apart more difficult. So therefore, some of these methods are best used together in order to back up and confirm data that they get through the use of one method. Through the use of these different methods, many different types of speciation can be explained, such as: duplication, sympatric, peripatric and many other different speciation events and types. (Ronquist and Sanmartin 2011) If we are able to better understand how certain species are related then we are better able to understand where life started and how it has evolved. This evolution can open up doors to understanding more clearly what the world was like before written records. I will cover each one of these different ways and how they could potentially be used in research that has occurred. The first way that cladogenesis is studied is through the use of simulations. In a paper by Phillimore and Price, they use simulations to study the possibility of the density of a population of different species of birds having an effect on the amount of more speciation that can occur for the birds. This method of study, first off, takes a known genus of birds and uses their mitochondrial protein coding genes, which are documented for reference, and watches to see if higher densities will cause more of less of a speciation amongst the bird genus. (Phillimore and Price 2008) This is a prime example of how simulations can be used to study the process of cladogenesis. Sometimes it’s just not practical to try and do a multi-year study of one species to try and see if it diverges into two species, and instead it’s just much easier to allow a computer, with numerous different variables and equations preprogramed into it, to run a simulation given the information about the birds and different variables that can go into their changing environment to see if cladogenetic events take place or not. Simulations are a good way to develop theories about how cladogenetic events might have arisen amongst a population because a computer can run numerous examples and different scenarios that we, as humans, may never have been able to come up with without the use of a computer. Another very popular method of study of cladogenetic events is the use of models. Models can be a great aid to scientists who wish to study specific species like Barraclough, Hogan, and Vogler ,who used models and molecular evidence together to see if ecological factors effect cladogenetic events in a specific genus of Tiger Beetles. The scientists already had a basic idea of how the beetles would behave and reproduce so all they had to do was set up experiments to test and see if ecological factors changed the outcomes of their experiments. Using these experiments as models, they could relate the information and make inferences on the population as a whole. (Barraclough, Hogan, and Vogler 1999) Models can be a great aid to scientists because the models can give us a more accurate representation of what might happen throughout the actual species. Even though it does not test every single possibility that may occur in the species, it still gives a very good representation about how these different species amongst the genus may have arisen throughout the years. Another potential model that can be used are phylogeny trees. Phylogeny trees can be very powerful and useful tools for studying cladogenetic events. Phylogeny trees can be used to track the progress of a specific trait throughout the history of many organisms and then that can be compared against a tree that is constructed using a null hypothesis (which basically states that cladogenetic events occur randomly and independently of one another). The trees can also be backed up and confirmed through the use of molecular evidence. (Ree, 2005) In the paper written by Ree, he uses the method described above to try and distinguish if evolution varies along with the diversification rate. Using a phylogeny tree can be very useful in trying to track when new cladogenetic events may have arisen throughout history and using other evidence to try and back up the claim, scientists are able to explain if the event actually was cladogenetic or some other form of speciation. A couple more models that are discussed in another paper are the use of the pure-birth and the birth-death model. These two models can be very beneficial in their own ways however, the pure-birth model does have a drawback because the pure-birth model operates under the assumption that when new species evolve and become present in the population, they don’t die out. So this model may not be very realistic, whereas the birth-death model takes into consideration all deaths and extinctions of species, which is very realistic because we know that species go extinct and organisms die out all the time. (Zhaxybayeva and Gogarten 2004) Nonetheless, the pure-birth model is used as a comparison model when studying cladogenetic events throughout the history of different organisms. In the paper written by Zhaxybayeva and Gogarten, they try to use comparisons of pure-birth and birth-death models to try and explain the evolution of the three domains of life. A more complicated, but also more thorough, model that is used by some scientist when studying cladogenetic events is the Equal-rates Markov model. This model basically just takes into consideration every single different type of event that can occur within a given set of parameters. This is a good test to use as a comparison to any other sort of test that a scientist may want to run in order to check for his own cladogenetic events. The model can be used as a good null comparison because it takes into consideration every single different event that can occur. For example, Agapow and Purvis came up with numerous different equations of their own to try and calculate for how often speciation or cladogenetic events would occur and they compared these next to the markov model. So by being able to have something to compare their own equations to, they were able to find equations that would more closely represent the population as a whole. (Agapow and Purvis 2002) Another model that can be used when trying to study cladogenetic events is the, dispersal-extinction-cladogenesis (DEC) model. Basically, what this model takes into account is stated right in its name, and that would be the dispersal of two species and the possible extinction of one of them. In order for a speciation event to be consider under the cladogenesis category, the two species would have had to have separated by some means and repopulated separately of each other while still being alive at the same time, otherwise the event would fall under anagenesis. So scientists can use this model in order to see whether or not two species where alive at the same time and if there was a large enough dispersion between the two for the event to be considered cladogenesis. (Ree and Smith 2008) The use of molecular data and fossil evidence together can be a very strong tool as well. In a paper written by Strotz and Allen, they try to use fossil data first to try and establish whether two species were alive at the same time or not, and then using the molecular data that has been cataloged by other scientists, they are able to compare if these two species were actually independent species that were able to evolve and reproduce separately from each other. However, in the beginning, using the fossil evidence has its own drawbacks so the fossil evidence had to be used under certain assumptions, and then after the fossils were set as being present during the same period of time, then they were able to use the molecular data to try and establish cladogenetic events. (Strotz and Allen 2012) This method of study can mainly help us study past/extinct species and where they came form or how they even came about. As previously stated earlier, these methods can be used to describe and explain different events that happen in evolution that cause two separate species, such as allopatric speciation. Allopatric speciation can be explained by the DEC model because it takes into account the fact that two species, that are separated by a distance, can be formed from one species, thus making it a cladogenetic event. The methods stated above can try and help explain many different cladogenetic events. In conclusion, cladogenesis is a very interesting, yet sometimes very complicated, field of study. Scientists use many different methods in order to study different forms of speciation and whether or not it was cladogenetic or not. They can use simulations on computers to try and run every single possible event or variable that may have affected the species that would cause it to split into two. Scientists can also use models/experiments or observations of current species today to try and understand the different factors that go into speciation and how those come about as well and whether or not they themselves could be considered cladogenetic. Another method of studying cladognesis is the use of fossil records and molecular evidence together. The fossil records can help to establish whether or not two species, that seem similar in their fossils, were alive at the same period of time or not, and then the molecular evidence can be used to help back it up as well. However, we are always getting new technology and scientists are constantly coming up with new ways to try and study species and develop new equations to try and explain speciation events. So with the use of new technology and new methods of study being introduced by other scientists, many more questions can possibly be answered about many different species, and maybe even how all life on earth started and how all the different species came about on this planet. Resources

Agapow, P.M., and A., Purvis. 2002. Power of Eight Tree Shape Statistics to Detect Nonrandom Diversification: A Comparison by Simulation of Two Models of Cladogenesis. Systematic Biology 51: 866-872. Barraclough, T.G., J.E., Hogan, and A.P., Vogler. 1999. Testing whether ecological factors promote cladogenesis in a group of tiger beetles (Coleoptera: Cicindelidae). The Royal Society 266: 1061-1067. Phillimore, A.B., and T.D., Price. 2008. Density-Dependent Cladogenesis in Birds. PLoS Biology 6:483-489. Ree, R.H., and S. A., Smith. 2008. Maximum Likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis. Systematic Biology 57: 4-14. Ree, R.H. 2005. Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59: 257-265. Ronquist, F., and I., Sanmartin. 2011. Phylogenetic Methods in Biogeography. Annual Review of Ecology, Evolution, and Systematics 42: 441-464. Strotz, L.C., and A.P., Allen. 2012. Assessing the role of cladogenesis in macroevolution by intergrating fossil and molecular evidence. Proceedings of the National Academy of Sciences of the United States of America 110: 2904-2909 Zhaxybayeva, O., and J.P., Gogarten. 2004. Cladogenesis, coalescence and the evolution of the three domains of life. TRENDS in Genetics 20: 182-187