Question

1. what are some potential problems by relying on only one gene? What would be a better approach?

2.Why does parsimony yield sometimes more than one tree?

Answer 1

1. A applicant gene is a gene that may transmit to the construct of interest, given the role of the gene in a discrete biological pathway or findings from earlier studies.

Applicant genes are chosen on the basis of either their functional significance to the disease pathogenesis or their locations within chromosomal regions concerned in linkage studies. The test SNP pragmatic with greater than expected frequency in individuals with disease is either a functional, disease-causing variant (a direct association) or a nonfunctional variant that exhibits strong linkage disequilibrium (LD) with the functional variant (an indirect association). Factually, hundreds of association studies of SLE were published in the last century, which, however, uncovered a limited number of confirmed SLE susceptibility genes because of small sample collections and/or a lack of dense marker coverage. These limitations in linkage and candidate gene studies have hindered understanding of the pathways causally involved in disease pathogenesis.

One better approach is to look for databases for well-characterized proteins that have similar amino acid sequences to the protein encoded by a new gene, and from there utilize some of the methods to discover the gene's function further

An unconventional approach is called insertional mutagenesis. This process relies on the fact that exogenous DNA inserted randomly into the genome can produce mutations if the inserted fragment interrupts a gene or its regulatory sequences. The inserted DNA, whose sequence is known, then serves as a molecular tag that aids in the successive recognition and cloning of the disrupted gene

2. Parsimony is the principle that the simplest clarification that can explain the data is to be favored. In the analysis of phylogeny, parsimony means that a hypothesis of relationships that entails the smallest number of character changes is most likely to be correct.

For example, based on the morphological data, the tree at left below requires only seven evolutionary changes and, based on the available evidence, is a better hypothesis than the tree at right, which requires nine evolutionary changes. To find the tree that is most parsimonious, authors use computational force.

Visualize that we want to figure out the evolutionary relationships among just four taxa: A, B, C, and D. There are 15 different ways that those taxa could be related, shown below, and that number skyrockets as the number of taxa increases. For just 10 taxa, there are more than 34 million different possible trees.

Hence, Parsimony may yield more than one tree.