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 samples, characterized in that the abundances of a plurality of rRNA gene markers in said samples correlate 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 an rRNA marker in a first MDP with the abundance of the same rRNA marker in a second MDP, across said plurality of rRNA markers;   c) repeating step (b) with at least one other MDP;   d) identifying at least two MDPs whose abundances of said plurality of rRNA markers correlate with each other; and   e) identifying the at least two samples from which the at least two MDPs identified in step d) are derived.   
     
     
         46 . The method of  claim 45 , wherein the at least two MDPs identified in step d) have similar marker compositions. 
     
     
         47 . The method of  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. 
     
     
         48 . The method of  claim 45  or  47 , wherein the correlation is represented by a linear, curvilinear or non-linear relationship. 
     
     
         49 . The method according to  claim 45  or  47 , wherein the correlation is represented by a positive or negative relationship. 
     
     
         50 . The method according to  claim 45 , wherein the plurality of rRNA markers comprises every rRNA marker in the MDP database. 
     
     
         51 . The method according to  claim 45 , wherein the plurality of rRNA markers comprises two or more rRNA markers whose abundances correlate with each other, said two or more markers being selected according to 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) selecting two or more rRNA markers whose abundances correlate with each other.   
     
     
         52 . The method according to  claim 45 , wherein the abundances of said plurality of rRNA markers correlate with the abundance of at least one sample parameter. 
     
     
         53 . 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. 
     
     
         54 . The method according to any one of  claims 45 ,  47  and  50 - 53 , wherein said rRNA marker abundance is an abundance relative to the total abundance of the plurality of rRNA markers in the sample. 
     
     
         55 . The method according to any one of  claims 45 ,  47  and  50 - 53 , wherein said microbial rRNA gene is a 16S rRNA gene. 
     
     
         56 . The method according to any one of  claims 45 ,  47  and  50 - 53 , wherein said microbial rRNA gene polymorphic sequence is from the intergenic region between a 16S rRNA gene and a 23S rRNA gene. 
     
     
         57 . The method according to any one of  claims 45 ,  47  and  50 - 53 , 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. 
     
     
         58 . The method according to  claim 57 , wherein the sample is obtained from the group consisting of: an oil reservoir, a gas reservoir, a building and a roadway. 
     
     
         59 . The method according to any one of  claims 45 ,  47  and  50 - 53 , 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.