A. Chapter 26 Section 4 Summary

          The purpose of molecular clocks is to help scientists estimate evolutionary time. With this, they can determine when different species diverged from each other in the past. The concept of a molecular clock is based upon the idea in the neutral theory of evolution (Sid talked about this) and that neutral mutations occur at a relatively constant rate. The theory also says that most genetic variation is due to the accumulation of neutral mutations. Therefore, if you know the rate at which neutral mutations occur, then you could find when two species diverged. In order to calibrate the clock and find the rate, scientists must use a known, like the fossil record. The fossil record helps them to determine the date when the last common ancestor between two species was alive.

          Unfortunately, this hypothesis is not completely correct. Not all DNA everywhere is every organism mutates at the exact same rate. Instead, there are certain genes and protein sequences that do seem to mutate at the same rate across taxa. Even with this, there are still exceptions, but generally, it is true. . Broadly speaking, the evolution of important genes occurs more slowly than that of genes with less vital functions. More rapidly changing genes are used to date more recent evolutionary events, and slower evolving genes are used to map more ancient divergences . One example is SSU rRNA, a gene that encodes an RNA found in the small ribosomal subunit. This gene was established very early on in the evolution of life because it is found in all living organisms. Its sequence has changed very slowly. This makes it useful for evaluating distant evolutionary relationships. On the other hand, mitochondrial genome and DNA sequences change very frequently during evolution. These would be better used for recent evolutionary relationships.

          Molecular clocks do not look like typical clocks. They are displayed as linear graphs. The y-axis is a measure of the number of nucleotide differences in a homologous gene between different pairs of species. The x-axis plots the amount of time that has elapsed since each pair of species shared a common ancestor. Over a defined period of time, the graph is linear, however over a larger span, evolutionary biologists believe that the line would not be as straight. This could be a result of differences in the generation times of the species being analyzed or variation in mutation rates between different species.

B. Prezi

C. Useful Materials

• Molecular Clocks: Four Decades of Evolution(this should link to a pdf file)- This is an article about the creation of molecular clocks in the 1960's and how they have been changing and evolving ever since. It is eight pages of information, including a timeline and many examples of specific cases scientists have worked on over the years. It is very extensive and detailed and really helps you to understand molecular clocks a lot better if you can follow the text and understand what the author is saying. The majority of the article talks about the problems and debates about the molecular clock as it was being created. DNA-sequencing techniques were not available until the mid-to late 70's so prior to that scientists had been using other methods.  The fossil record was also less reliable then. Both of these factors caused a lot of debate varying results. However, when PCR was invented in 1985 and DNA sequences could be compared base by base, the hypothesis gained a lot more validity.  Today, it is generally accepted since it has been being used to date evolutionary relationships for so long. The picture below is included in the pdf. It shows the increase in the use of molecular clocks

                                                                      .

• A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea.  This is a PubMed article about the evolution of cetacea, which is a clade (Ambika's section) of marine mammals, including dolphins, porpoises and whales. In order to learn more about this clade, the scientists wanted to create a well developed phylogenetic tree because although a large amount of molecular data has been collected, the molecular clock hypothesis has not yet been applied and their DNA sequences have not been directly integrated with the fossil record. They compared new DNA sequences of the extinct Yangtze River dolphin with other published information. By using the parsimony method (John's section) they found that the Yangtze River dolphin had evolutionary relationships with 74 taxas (Lauren's section), which included all living families and 11 extinct families of Cetacea. They then continued and dated some of cetacean diversification by using the fossil record. They sorted out their information of phylogenetic trees which showed that many characteristics shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats      

This is a Yangtze River Dolphin. It is now extinct. In the article, they used the molecular clock method to date when it evolved from other Cetacea.	This is a bottle nose dolphin. It is evolutionary related to the Yangtze River Dolphin.

• Probing question: What is a molecular clock? This is a short article about molecular clocks. If you don't understand what the book is saying, this article is simple and straightforward. Unfortunately, I could find no videos or fun animations about molecular clocks so if you don't understand it you are going to have to read. It is almost a perfect summary of what the book says. I used this article to try to grasp my topic. 

• Molecular Clocks This is another short passage about molecular clocks. It is even shorter than the one above, but it gives a good example of how molecular clocks are used by showing pictures of nucleotide sequences and neutral mutations in them.

C. Virtual Lecture

VirtualLecture.mp4