DNA technology has revolutionized the study of biological relationships. Cladistics, a method of inferring evolutionary relationships based on shared derived characters, has been particularly affected. DNA sequences can be used to reconstruct phylogenies with much greater precision than was possible using morphology alone. In addition, DNA data can be used to generate new hypotheses about relationships that can be tested using traditional methods.
The increased use of cladistics can be traced to several factors. First, the availability of DNA sequence data has exploded in recent years. Second, the methods used to infer phylogenies from DNA data have become more sophisticated. And third, the use of cladistics has been promoted by a number of influential researchers.
The following sections will discuss each of these factors in turn.
The availability of DNA sequence data
The first factor that has led to the increased use of cladistics is the availability of DNA sequence data. In the early days of molecular phylogenetics, only a few genes were available for analysis. Today, there are databases with billions of base pairs of DNA sequence data.
This increase in data has had a number of consequences. First, it has allowed researchers to reconstruct phylogenies with much greater precision. Second, it has allowed for the analysis of a wider range of characters, including those that are non-coding. And third, it has allowed for the analysis of a wider range of taxa, including those that are not closely related.
The methods used to infer phylogenies from DNA data
The second factor that has led to the increased use of cladistics is the methods used to infer phylogenies from DNA data. In the early days of molecular phylogenetics, the only method available was the neighbor-joining method. This method is still used today, but it has been superseded by more sophisticated methods, such as maximum likelihood and Bayesian inference.
These newer methods have a number of advantages over the neighbor-joining method. First, they can take into account the uncertainty in the data. Second, they can handle a larger number of taxa and characters. And third, they can be used to test hypotheses about relationships.
The use of cladistics
The third factor that has led to the increased use of cladistics is the use of cladistics by a number of influential researchers. In the early days of molecular phylogenetics, the use of cladistics was limited to a few researchers. Today, the use of cladistics is widespread.
The use of cladistics has been promoted by a number of influential researchers, including Douglas Hofstadter, Ernst Mayr, and Jerry Coyne. Hofstadter and Mayr are both biologists who have written about the importance of cladistics. Coyne is a physicist who has written about the use of cladistics in resolving the disputed relationships of the vertebrates.
The increased use of cladistics has led to the development of a number of new methods and software packages. These methods and software packages have made cladistics more accessible to researchers who are not specialists in the field.
The following sections will discuss some of the methods and software packages that have been developed.
Methods
There are a number of methods that have been developed for inferring phylogenies from DNA data. These methods can be divided into two categories: those that use distance methods and those that use parsimony methods.
Distance methods
Distance methods are methods that use a distance metric to infer phylogenies. The most common distance metric is the Jukes-Cantor distance. Other distance metrics that have been used include the Kimura two-parameter distance and the Tamura-Nei distance.
Parsimony methods
Parsimony methods are methods that use a parsimony criterion to infer phylogenies. The most common parsimony criterion is the minimum evolution criterion. Other parsimony criteria that have been used include the maximum likelihood criterion and the Bayesian criterion.
Software packages
There are a number of software packages that have been developed for inferring phylogenies from DNA data. These software packages can be divided into two categories: those that use distance methods and those that use parsimony methods.
Distance methods
There are a number of software packages that use distance methods to infer phylogenies. The most popular of these is PHYLIP. Other software packages that use distance methods include PAUP* and Mega.
Parsimony methods
There are a number of software packages that use parsimony methods to infer phylogenies. The most popular of these is PAUP*. Other software packages that use parsimony methods include PHYLIP and Mega.
Conclusion
In conclusion, DNA technology has led to the increased use of cladistics. This increase can be traced to the availability of DNA sequence data, the methods used to infer phylogenies from DNA data, and the use of cladistics by a number of influential researchers.
