Methods for the survey and genetic analysis of populations

Abstract

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

1 - 44 . (canceled) 
     
     
         45 . A method of identifying two or more rRNA markers from a plurality of samples, the abundances of said rRNA markers correlating with one another, the method comprising the steps of:
 a) providing a Marker Diversity Profile (MDP) database comprising a plurality of MDPs derived from a plurality of samples, each MDP being derived from one sample, wherein each MDP comprises the abundances, in said sample, of a plurality of rRNA markers, and   wherein each of said rRNA markers comprises a microbial rRNA gene polymorphic sequence;   b) performing a correlation analysis of the abundance of a first rRNA marker in an MDP with other rRNA markers in the same MDP, across said plurality of MPDs;   c) identifying two or more rRNA markers whose abundances correlate with each other.   
     
     
         46 . The method according to  claim 45 , wherein the correlation is determined using a graphical representation of the abundances of the plurality of rRNA markers from the plurality of samples. 
     
     
         47 . The method according to  claim 45  or  46 , wherein the correlation is represented by a linear, curvilinear or non-linear relation. 
     
     
         48 . The method according to  claim 45  or  46 , wherein the correlation is represented by a positive or negative relationship. 
     
     
         49 . The method according to  claim 45 , further comprising the step of creating a dendrogram that reflects the relative level of correlation between each rRNA marker and every other rRNA marker in the MDP database. 
     
     
         50 . The method according to  claim 45 , further comprising the step of creating a pairwise correlation matrix of each rRNA marker with every other rRNA marker in the MDP database. 
     
     
         51 . The method according to  claim 45 , wherein the correlation is expressible by a correlation value that is selected from the group consisting of at least 0.5, at least 0.6, at least 0.7, at least 0.8, at least 0.9 and at least 0.95. 
     
     
         52 . The method according to any one of  claims 45 ,  46  and  49 - 51 , wherein said rRNA marker abundance is an abundance relative to the total abundance of the plurality of rRNA markers in the sample. 
     
     
         53 . The method according to any one of  claims 45 ,  46  and  49 - 51 , wherein said microbial rRNA gene is a 16S rRNA gene. 
     
     
         54 . The method according to any one of  claims 45 ,  46  and  49 - 51 , wherein said microbial rRNA gene polymorphic sequence is from the intergenic region between a 16S rRNA gene and a 23S rRNA gene. 
     
     
         55 . The method according to any one of  claims 45 ,  46  and  49 - 51 , wherein the sample is selected from the group consisting of: a soil sample, a rock sample, a water sample, an air sample, a hydrocarbon sample, a petroleum sample and a biofilm sample. 
     
     
         56 . The method according to  claim 55 , wherein the sample is obtained from the group consisting of: an oil reservoir, a gas reservoir, a building and a roadway. 
     
     
         57 . The method according to any one of  claims 45 ,  46  and  49 - 51 , wherein the sample is obtained from the group consisting of: a human, a plant, an animal, a body tissue sample, a body fluid sample, a foodstuff, a cell culture and a tissue culture.