To whet our appetite for sequence analysis, we will simply compute what percentage of the base pairs we compared are identical to each other. How do we define what is 'similar'? There are myriad ways of scoring sequence similarity and is a subject that people have thought very deeply about. This means that we will have to ignore any gaps in the sequence (denoted by ' -' signifying an insertion or deletion in the reference genome). To do so, we'll simplify our analysis to only compare the number of mismatches at a given position in the sequence.
We'll compare the sequences from our skink on Fernando de Noronha to those in other regions of the world.
#Dna sequence analysis how to#
We will learn how to read in the DNA sequences and score them by the similarity of their sequence to test this hypothesis. Arnold who sequenced a component of the mitochondrial DNA from a large variety of skinks across the world and from Fernando de Noronha. In this tutorial, we will use the data from S. This placement was not performed through morphology but through DNA sequence analysis. While the exact trajectory of this 'improbable voyage' is still up for debate, the phylogenetic placement of this species is fairly certain. How did they arrive at the island? In 1888, Alfred Russel Wallace proposed that perhaps the skink arrived on the archipelago by floating on a raft of vegetation across the open ocean, although this trip was estimated to take around 150 days using the knowledge of the oceanic currents from Africa to South America, as is shown in the figure below. Because the archipelago was formed from volcanoes, there was no way that these lizards traveled to the island by land. One curious inhabitant of the archipelago is Mabuya atlantica (also known as the Noronha skink), which is phylogenetically placed along with the African species of Trachylepis.
The twenty one islands and islets of this archipelago are volcanic in origin and have many endemic plant and animal species. Approximately 200 miles off the coast of Brazil exists a small (and quite beautiful) archipelago named Fernando de Noronha.